Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c250' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6965707-fedora-39-ppc64le --chroot fedora-39-ppc64le Version: 0.70 PID: 6260 Logging PID: 6261 Task: {'appstream': False, 'background': True, 'build_id': 6965707, 'buildroot_pkgs': [], 'chroot': 'fedora-39-ppc64le', 'enable_net': False, 'fedora_review': False, 'git_hash': 'd9276f3ea0b26ef86c19cc9a0240e46ff4bcfdad', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/seqan', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'seqan', 'package_version': '1.4.2-53', 'project_dirname': 'openblas-0.3.23', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-ppc64le/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/releng', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/releng', 'tags': [], 'task_id': '6965707-fedora-39-ppc64le', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/seqan /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/seqan', '/var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan'... Running: git checkout d9276f3ea0b26ef86c19cc9a0240e46ff4bcfdad -- cmd: ['git', 'checkout', 'd9276f3ea0b26ef86c19cc9a0240e46ff4bcfdad', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan rc: 0 stdout: stderr: Note: switching to 'd9276f3ea0b26ef86c19cc9a0240e46ff4bcfdad'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at d9276f3 automatic import of seqan Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading seqan-src-1.4.2.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o seqan-src-1.4.2.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23/seqan/seqan-src-1.4.2.tar.gz/md5/e7d2c6cf6474b5186c27ec31bd32738a/seqan-src-1.4.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 115M 100 115M 0 0 46.8M 0 0:00:02 0:00:02 --:--:-- 46.8M INFO: Reading stdout from command: md5sum seqan-src-1.4.2.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan/seqan.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706322988.398155 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan/seqan.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706322988.398155 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan/seqan.spec) Config(fedora-39-ppc64le) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-ppc64le-bootstrap-1706322988.398155/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-ppc64le-bootstrap-1706322988.398155/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/5e71cf379ce8c11c753d74dd3fd8330d085628218bb73dc81a51ff6d47689e47/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/5e71cf379ce8c11c753d74dd3fd8330d085628218bb73dc81a51ff6d47689e47/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 19 MB/s | 24 MB 00:01 Additional repo http_kojipkgs_fedoraproject_org 47 MB/s | 71 MB 00:01 fedora 13 MB/s | 83 MB 00:06 updates 8.0 MB/s | 26 MB 00:03 Last metadata expiration check: 0:00:12 ago on Sat Jan 27 02:38:24 2024. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================== Package Arch Version Repository Size ========================================================================================================================== Installing: python3-dnf-plugins-core noarch 4.4.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 496 k dnf-data noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k python3-dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 549 k yum noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs ppc64le 1:1.14.10-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 177 k python3-dateutil noarch 1:2.8.2-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus ppc64le 1.3.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 150 k python3-distro noarch 1.9.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k python3-six noarch 1.16.0-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd ppc64le 235-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 102 k Transaction Summary ========================================================================================================================== Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): dbus-libs-1.14.10-1.fc40.ppc64le.rpm 1.4 MB/s | 177 kB 00:00 (2/11): python3-distro-1.9.0-1.fc40.noarch.rpm 715 kB/s | 45 kB 00:00 (3/11): python3-dbus-1.3.2-4.fc39.ppc64le.rpm 753 kB/s | 150 kB 00:00 (4/11): python3-dateutil-2.8.2-11.fc40.noarch.r 1.5 MB/s | 345 kB 00:00 (5/11): python3-six-1.16.0-12.fc39.noarch.rpm 938 kB/s | 41 kB 00:00 (6/11): python3-dnf-plugins-core-4.4.4-1.fc40.n 3.8 MB/s | 302 kB 00:00 (7/11): python3-systemd-235-5.fc39.ppc64le.rpm 2.0 MB/s | 102 kB 00:00 (8/11): dnf-4.18.2-1.fc40.noarch.rpm 5.6 MB/s | 496 kB 00:00 (9/11): dnf-data-4.18.2-1.fc40.noarch.rpm 634 kB/s | 39 kB 00:00 (10/11): yum-4.18.2-1.fc40.noarch.rpm 564 kB/s | 37 kB 00:00 (11/11): python3-dnf-4.18.2-1.fc40.noarch.rpm 3.5 MB/s | 549 kB 00:00 -------------------------------------------------------------------------------- Total 5.2 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.18.2-1.fc40.noarch 1/15 Upgrading : python3-dnf-4.18.2-1.fc40.noarch 2/15 Upgrading : dnf-4.18.2-1.fc40.noarch 3/15 Running scriptlet: dnf-4.18.2-1.fc40.noarch 3/15 Installing : python3-systemd-235-5.fc39.ppc64le 4/15 Installing : python3-six-1.16.0-12.fc39.noarch 5/15 Installing : python3-dateutil-1:2.8.2-11.fc40.noarch 6/15 Installing : python3-distro-1.9.0-1.fc40.noarch 7/15 Installing : dbus-libs-1:1.14.10-1.fc40.ppc64le 8/15 Installing : python3-dbus-1.3.2-4.fc39.ppc64le 9/15 Installing : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 10/15 Upgrading : yum-4.18.2-1.fc40.noarch 11/15 Cleanup : yum-4.18.1-2.fc39.noarch 12/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : dnf-4.18.1-2.fc39.noarch 13/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : python3-dnf-4.18.1-2.fc39.noarch 14/15 Cleanup : dnf-data-4.18.1-2.fc39.noarch 15/15 Running scriptlet: dnf-data-4.18.1-2.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-1.fc40.ppc64le 1/15 Verifying : python3-dateutil-1:2.8.2-11.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-4.fc39.ppc64le 3/15 Verifying : python3-distro-1.9.0-1.fc40.noarch 4/15 Verifying : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 5/15 Verifying : python3-six-1.16.0-12.fc39.noarch 6/15 Verifying : python3-systemd-235-5.fc39.ppc64le 7/15 Verifying : dnf-4.18.2-1.fc40.noarch 8/15 Verifying : dnf-4.18.1-2.fc39.noarch 9/15 Verifying : dnf-data-4.18.2-1.fc40.noarch 10/15 Verifying : dnf-data-4.18.1-2.fc39.noarch 11/15 Verifying : python3-dnf-4.18.2-1.fc40.noarch 12/15 Verifying : python3-dnf-4.18.1-2.fc39.noarch 13/15 Verifying : yum-4.18.2-1.fc40.noarch 14/15 Verifying : yum-4.18.1-2.fc39.noarch 15/15 Upgraded: dnf-4.18.2-1.fc40.noarch dnf-data-4.18.2-1.fc40.noarch python3-dnf-4.18.2-1.fc40.noarch yum-4.18.2-1.fc40.noarch Installed: dbus-libs-1:1.14.10-1.fc40.ppc64le python3-dateutil-1:2.8.2-11.fc40.noarch python3-dbus-1.3.2-4.fc39.ppc64le python3-distro-1.9.0-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.ppc64le Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.ppc64le rpm-sequoia-1.5.0-1.fc39.ppc64le python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 27 MB/s | 24 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 25 MB/s | 71 MB 00:02 fedora 18 MB/s | 83 MB 00:04 updates 9.3 MB/s | 26 MB 00:02 Last metadata expiration check: 0:00:11 ago on Sat Jan 27 02:40:30 2024. Dependencies resolved. ========================================================================================================================================= Package Arch Version Repository Size ========================================================================================================================================= Installing group/module packages: bash ppc64le 5.2.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 M bzip2 ppc64le 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 53 k coreutils ppc64le 9.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M cpio ppc64le 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 293 k diffutils ppc64le 3.10-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 399 k fedora-release-common noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k findutils ppc64le 1:4.9.0-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 531 k gawk ppc64le 5.3.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M glibc-minimal-langpack ppc64le 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96 k grep ppc64le 3.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 297 k gzip ppc64le 1.12-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 163 k info ppc64le 7.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 203 k patch ppc64le 2.7.6-22.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 137 k redhat-rpm-config noarch 280-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build ppc64le 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 73 k sed ppc64le 4.8-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 303 k shadow-utils ppc64le 2:4.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M tar ppc64le 2:1.35-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 874 k unzip ppc64le 6.0-62.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 190 k util-linux ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M which ppc64le 2.21-40.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k xz ppc64le 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 535 k Installing dependencies: alternatives ppc64le 1.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k ansible-srpm-macros noarch 1-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs ppc64le 4.0-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 135 k authselect ppc64le 1.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 145 k authselect-libs ppc64le 1.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 239 k basesystem noarch 11-18.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k binutils ppc64le 2.41-30.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.3 M binutils-gold ppc64le 2.41-30.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M bzip2-libs ppc64le 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 47 k ca-certificates noarch 2023.2.62_v7.0.401-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 863 k coreutils-common ppc64le 9.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib ppc64le 2.9.11-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85 k crypto-policies noarch 20231204-1.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69 k curl ppc64le 8.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 373 k cyrus-sasl-lib ppc64le 2.1.28-17.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 875 k debugedit ppc64le 5.0-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 81 k dwz ppc64le 0.15-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 147 k ed ppc64le 1.20-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85 k efi-srpm-macros noarch 5-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k elfutils ppc64le 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 575 k elfutils-debuginfod-client ppc64le 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k elfutils-default-yama-scope noarch 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k elfutils-libelf ppc64le 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 203 k elfutils-libs ppc64le 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 295 k fedora-gpg-keys noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 119 k fedora-release noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10 k fedora-release-identity-basic noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 k fedora-repos noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.3 k fedora-repos-rawhide noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.9 k file ppc64le 5.45-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 50 k file-libs ppc64le 5.45-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 774 k filesystem ppc64le 3.18-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26 k forge-srpm-macros noarch 0.2.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k fpc-srpm-macros noarch 1.3-8.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.4 k gdb-minimal ppc64le 14.1-7.fc40 copr_base 4.2 M gdbm ppc64le 1:1.23-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 156 k gdbm-libs ppc64le 1:1.23-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 62 k ghc-srpm-macros noarch 1.6.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.1 k glibc ppc64le 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.3 M glibc-common ppc64le 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 391 k glibc-gconv-extra ppc64le 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 M gmp ppc64le 1:6.2.1-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 304 k gnat-srpm-macros noarch 6-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.8 k go-srpm-macros noarch 3.3.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 k jansson ppc64le 2.13.1-7.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 49 k kernel-srpm-macros noarch 1.0-20.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10 k keyutils-libs ppc64le 1.6.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 33 k krb5-libs ppc64le 1.21.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 838 k libacl ppc64le 2.3.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k libarchive ppc64le 3.7.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 477 k libattr ppc64le 2.5.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k libblkid ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 132 k libbrotli ppc64le 1.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 380 k libcap ppc64le 2.69-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 89 k libcap-ng ppc64le 0.8.4-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k libcom_err ppc64le 1.47.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k libcurl ppc64le 8.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 382 k libeconf ppc64le 0.5.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k libevent ppc64le 2.1.12-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 275 k libfdisk ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 176 k libffi ppc64le 3.4.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k libgcc ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 93 k libgomp ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k libidn2 ppc64le 2.3.4-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 114 k libmount ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 176 k libnghttp2 ppc64le 1.59.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85 k libnsl2 ppc64le 2.0.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k libpkgconf ppc64le 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k libpsl ppc64le 0.21.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 65 k libpwquality ppc64le 1.4.5-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112 k librtas ppc64le 2.0.4-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 70 k libselinux ppc64le 3.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k libsemanage ppc64le 3.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 128 k libsepol ppc64le 3.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 370 k libsmartcols ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 74 k libssh ppc64le 0.10.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 240 k libssh-config noarch 0.10.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.1 k libstdc++ ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M libtasn1 ppc64le 4.19.0-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 80 k libtirpc ppc64le 1.3.4-1.rc1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 108 k libunistring ppc64le 1.1-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 578 k libutempter ppc64le 1.2.1-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k libuuid ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 30 k libverto ppc64le 0.3.2-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k libxcrypt ppc64le 4.4.36-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 131 k libxml2 ppc64le 2.12.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 765 k libzstd ppc64le 1.5.5-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 336 k lua-libs ppc64le 5.4.6-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 149 k lua-srpm-macros noarch 1-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.6 k lz4-libs ppc64le 1.9.4-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85 k mpfr ppc64le 4.2.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 353 k ncurses-base noarch 6.4-9.20240113.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 63 k ncurses-libs ppc64le 6.4-9.20240113.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 378 k ocaml-srpm-macros noarch 9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.0 k openblas-srpm-macros noarch 2-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.5 k openldap ppc64le 2.6.6-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 287 k openssl-libs ppc64le 1:3.1.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.3 M p11-kit ppc64le 0.25.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 507 k p11-kit-trust ppc64le 0.25.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 157 k package-notes-srpm-macros noarch 0.5-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 k pam ppc64le 1.6.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 562 k pam-libs ppc64le 1.6.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 63 k pcre2 ppc64le 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 241 k pcre2-syntax noarch 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 143 k perl-srpm-macros noarch 1-51.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 k pkgconf ppc64le 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k pkgconf-m4 noarch 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k pkgconf-pkg-config ppc64le 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.6 k popt ppc64le 1.19-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 64 k publicsuffix-list-dafsa noarch 20240107-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 58 k pyproject-srpm-macros noarch 1.12.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k python-srpm-macros noarch 3.12-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 24 k qt5-srpm-macros noarch 5.15.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.4 k qt6-srpm-macros noarch 6.6.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.8 k readline ppc64le 8.2-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 230 k rpm ppc64le 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 511 k rpm-build-libs ppc64le 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103 k rpm-libs ppc64le 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 357 k rpm-sequoia ppc64le 1.6.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 M rust-srpm-macros noarch 25.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k setup noarch 2.14.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 148 k sqlite-libs ppc64le 3.45.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 817 k systemd-libs ppc64le 255.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 751 k util-linux-core ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 533 k xxhash-libs ppc64le 0.8.2-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k xz-libs ppc64le 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k zig-srpm-macros noarch 1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 k zip ppc64le 3.0-39.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274 k zlib-ng-compat ppc64le 2.1.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 78 k zstd ppc64le 1.5.5-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 499 k Installing Groups: Buildsystem building group Transaction Summary ========================================================================================================================================= Install 153 Packages Total download size: 56 M Installed size: 323 M Downloading Packages: (1/153): alternatives-1.26-1.fc40.ppc64le.rpm 184 kB/s | 42 kB 00:00 (2/153): ansible-srpm-macros-1-12.fc40.noarch.r 91 kB/s | 21 kB 00:00 (3/153): gdb-minimal-14.1-7.fc40.ppc64le.rpm 12 MB/s | 4.2 MB 00:00 (4/153): audit-libs-4.0-7.fc40.ppc64le.rpm 906 kB/s | 135 kB 00:00 (5/153): authselect-1.5.0-1.fc40.ppc64le.rpm 970 kB/s | 145 kB 00:00 (6/153): basesystem-11-18.fc39.noarch.rpm 184 kB/s | 7.2 kB 00:00 (7/153): authselect-libs-1.5.0-1.fc40.ppc64le.r 2.6 MB/s | 239 kB 00:00 (8/153): bash-5.2.26-1.fc40.ppc64le.rpm 9.1 MB/s | 1.9 MB 00:00 (9/153): bzip2-1.0.8-16.fc39.ppc64le.rpm 2.6 MB/s | 53 kB 00:00 (10/153): binutils-gold-2.41-30.fc40.ppc64le.rp 6.9 MB/s | 1.1 MB 00:00 (11/153): bzip2-libs-1.0.8-16.fc39.ppc64le.rpm 2.1 MB/s | 47 kB 00:00 (12/153): coreutils-9.4-3.fc40.ppc64le.rpm 29 MB/s | 1.4 MB 00:00 (13/153): coreutils-common-9.4-3.fc40.ppc64le.r 34 MB/s | 2.1 MB 00:00 (14/153): cpio-2.15-1.fc40.ppc64le.rpm 12 MB/s | 293 kB 00:00 (15/153): ca-certificates-2023.2.62_v7.0.401-4. 5.8 MB/s | 863 kB 00:00 (16/153): crypto-policies-20231204-1.git1e3a2e4 3.6 MB/s | 69 kB 00:00 (17/153): cracklib-2.9.11-2.fc39.ppc64le.rpm 2.2 MB/s | 85 kB 00:00 (18/153): binutils-2.41-30.fc40.ppc64le.rpm 15 MB/s | 6.3 MB 00:00 (19/153): curl-8.5.0-2.fc40.ppc64le.rpm 8.2 MB/s | 373 kB 00:00 (20/153): debugedit-5.0-12.fc40.ppc64le.rpm 2.1 MB/s | 81 kB 00:00 (21/153): diffutils-3.10-3.fc39.ppc64le.rpm 10 MB/s | 399 kB 00:00 (22/153): dwz-0.15-3.fc39.ppc64le.rpm 5.0 MB/s | 147 kB 00:00 (23/153): ed-1.20-1.fc40.ppc64le.rpm 2.6 MB/s | 85 kB 00:00 (24/153): efi-srpm-macros-5-9.fc39.noarch.rpm 493 kB/s | 22 kB 00:00 (25/153): elfutils-debuginfod-client-0.190-4.fc 1.0 MB/s | 39 kB 00:00 (26/153): elfutils-0.190-4.fc40.ppc64le.rpm 4.6 MB/s | 575 kB 00:00 (27/153): elfutils-default-yama-scope-0.190-4.f 310 kB/s | 13 kB 00:00 (28/153): elfutils-libelf-0.190-4.fc40.ppc64le. 4.7 MB/s | 203 kB 00:00 (29/153): fedora-gpg-keys-40-0.2.noarch.rpm 3.0 MB/s | 119 kB 00:00 (30/153): fedora-release-40-0.29.noarch.rpm 209 kB/s | 10 kB 00:00 (31/153): fedora-release-common-40-0.29.noarch. 455 kB/s | 21 kB 00:00 (32/153): fedora-release-identity-basic-40-0.29 136 kB/s | 11 kB 00:00 (33/153): fedora-repos-40-0.2.noarch.rpm 157 kB/s | 9.3 kB 00:00 (34/153): cyrus-sasl-lib-2.1.28-17.fc40.ppc64le 1.5 MB/s | 875 kB 00:00 (35/153): fedora-repos-rawhide-40-0.2.noarch.rp 423 kB/s | 8.9 kB 00:00 (36/153): file-5.45-1.fc40.ppc64le.rpm 856 kB/s | 50 kB 00:00 (37/153): file-libs-5.45-1.fc40.ppc64le.rpm 13 MB/s | 774 kB 00:00 (38/153): findutils-4.9.0-6.fc40.ppc64le.rpm 15 MB/s | 531 kB 00:00 (39/153): fonts-srpm-macros-2.0.5-12.fc39.noarc 415 kB/s | 26 kB 00:00 (40/153): forge-srpm-macros-0.2.0-1.fc40.noarch 375 kB/s | 18 kB 00:00 (41/153): fpc-srpm-macros-1.3-8.fc39.noarch.rpm 149 kB/s | 7.4 kB 00:00 (42/153): elfutils-libs-0.190-4.fc40.ppc64le.rp 433 kB/s | 295 kB 00:00 (43/153): gawk-5.3.0-1.fc40.ppc64le.rpm 10 MB/s | 1.1 MB 00:00 (44/153): gdbm-libs-1.23-4.fc39.ppc64le.rpm 1.5 MB/s | 62 kB 00:00 (45/153): ghc-srpm-macros-1.6.1-3.fc40.noarch.r 380 kB/s | 8.1 kB 00:00 (46/153): gdbm-1.23-4.fc39.ppc64le.rpm 1.7 MB/s | 156 kB 00:00 (47/153): glibc-2.38.9000-35.fc40.ppc64le.rpm 23 MB/s | 2.3 MB 00:00 (48/153): glibc-common-2.38.9000-35.fc40.ppc64l 2.6 MB/s | 391 kB 00:00 (49/153): filesystem-3.18-6.fc39.ppc64le.rpm 1.9 MB/s | 1.1 MB 00:00 (50/153): glibc-gconv-extra-2.38.9000-35.fc40.p 21 MB/s | 2.0 MB 00:00 (51/153): glibc-minimal-langpack-2.38.9000-35.f 1.6 MB/s | 96 kB 00:00 (52/153): gnat-srpm-macros-6-3.fc39.noarch.rpm 325 kB/s | 8.8 kB 00:00 (53/153): go-srpm-macros-3.3.1-1.fc40.noarch.rp 1.2 MB/s | 28 kB 00:00 (54/153): grep-3.11-5.fc40.ppc64le.rpm 10 MB/s | 297 kB 00:00 (55/153): gzip-1.12-6.fc39.ppc64le.rpm 4.0 MB/s | 163 kB 00:00 (56/153): info-7.1-1.fc40.ppc64le.rpm 6.1 MB/s | 203 kB 00:00 (57/153): gmp-6.2.1-5.fc39.ppc64le.rpm 2.8 MB/s | 304 kB 00:00 (58/153): jansson-2.13.1-7.fc39.ppc64le.rpm 1.5 MB/s | 49 kB 00:00 (59/153): kernel-srpm-macros-1.0-20.fc39.noarch 519 kB/s | 10 kB 00:00 (60/153): keyutils-libs-1.6.3-1.fc40.ppc64le.rp 1.0 MB/s | 33 kB 00:00 (61/153): libacl-2.3.2-1.fc40.ppc64le.rpm 893 kB/s | 27 kB 00:00 (62/153): krb5-libs-1.21.2-3.fc40.ppc64le.rpm 9.4 MB/s | 838 kB 00:00 (63/153): libattr-2.5.2-1.fc40.ppc64le.rpm 250 kB/s | 19 kB 00:00 (64/153): libblkid-2.39.3-4.fc40.ppc64le.rpm 1.7 MB/s | 132 kB 00:00 (65/153): libcap-2.69-1.fc40.ppc64le.rpm 1.5 MB/s | 89 kB 00:00 (66/153): libbrotli-1.1.0-1.fc40.ppc64le.rpm 1.9 MB/s | 380 kB 00:00 (67/153): libcap-ng-0.8.4-2.fc40.ppc64le.rpm 411 kB/s | 34 kB 00:00 (68/153): libarchive-3.7.2-1.fc40.ppc64le.rpm 1.5 MB/s | 477 kB 00:00 (69/153): libcom_err-1.47.0-2.fc39.ppc64le.rpm 698 kB/s | 27 kB 00:00 (70/153): libeconf-0.5.2-1.fc40.ppc64le.rpm 689 kB/s | 34 kB 00:00 (71/153): libevent-2.1.12-9.fc39.ppc64le.rpm 4.5 MB/s | 275 kB 00:00 (72/153): libcurl-8.5.0-2.fc40.ppc64le.rpm 3.2 MB/s | 382 kB 00:00 (73/153): libffi-3.4.4-5.fc40.ppc64le.rpm 790 kB/s | 38 kB 00:00 (74/153): libfdisk-2.39.3-4.fc40.ppc64le.rpm 1.9 MB/s | 176 kB 00:00 (75/153): libgcc-14.0.1-0.3.fc40.ppc64le.rpm 1.9 MB/s | 93 kB 00:00 (76/153): libidn2-2.3.4-3.fc39.ppc64le.rpm 2.2 MB/s | 114 kB 00:00 (77/153): libmount-2.39.3-4.fc40.ppc64le.rpm 2.0 MB/s | 176 kB 00:00 (78/153): libnghttp2-1.59.0-1.fc40.ppc64le.rpm 1.1 MB/s | 85 kB 00:00 (79/153): libgomp-14.0.1-0.3.fc40.ppc64le.rpm 1.8 MB/s | 345 kB 00:00 (80/153): libnsl2-2.0.1-1.fc40.ppc64le.rpm 402 kB/s | 32 kB 00:00 (81/153): libpkgconf-1.9.5-2.fc39.ppc64le.rpm 547 kB/s | 42 kB 00:00 (82/153): libpwquality-1.4.5-6.fc39.ppc64le.rpm 1.6 MB/s | 112 kB 00:00 (83/153): libpsl-0.21.5-1.fc40.ppc64le.rpm 806 kB/s | 65 kB 00:00 (84/153): librtas-2.0.4-3.fc39.ppc64le.rpm 1.1 MB/s | 70 kB 00:00 (85/153): libsemanage-3.6-1.fc40.ppc64le.rpm 3.0 MB/s | 128 kB 00:00 (86/153): libselinux-3.6-2.fc40.ppc64le.rpm 1.1 MB/s | 101 kB 00:00 (87/153): libsepol-3.6-1.fc40.ppc64le.rpm 5.9 MB/s | 370 kB 00:00 (88/153): libsmartcols-2.39.3-4.fc40.ppc64le.rp 978 kB/s | 74 kB 00:00 (89/153): libssh-config-0.10.6-2.fc40.noarch.rp 161 kB/s | 9.1 kB 00:00 (90/153): libssh-0.10.6-2.fc40.ppc64le.rpm 2.2 MB/s | 240 kB 00:00 (91/153): libstdc++-14.0.1-0.3.fc40.ppc64le.rpm 14 MB/s | 1.0 MB 00:00 (92/153): libtasn1-4.19.0-3.fc39.ppc64le.rpm 1.4 MB/s | 80 kB 00:00 (93/153): libtirpc-1.3.4-1.rc1.fc40.ppc64le.rpm 2.7 MB/s | 108 kB 00:00 (94/153): libunistring-1.1-5.fc40.ppc64le.rpm 13 MB/s | 578 kB 00:00 (95/153): libutempter-1.2.1-10.fc39.ppc64le.rpm 624 kB/s | 27 kB 00:00 (96/153): libuuid-2.39.3-4.fc40.ppc64le.rpm 1.1 MB/s | 30 kB 00:00 (97/153): libverto-0.3.2-6.fc39.ppc64le.rpm 803 kB/s | 22 kB 00:00 (98/153): libxcrypt-4.4.36-4.fc40.ppc64le.rpm 2.0 MB/s | 131 kB 00:00 (99/153): libzstd-1.5.5-4.fc39.ppc64le.rpm 8.8 MB/s | 336 kB 00:00 (100/153): lua-libs-5.4.6-3.fc39.ppc64le.rpm 4.3 MB/s | 149 kB 00:00 (101/153): lua-srpm-macros-1-9.fc39.noarch.rpm 250 kB/s | 8.6 kB 00:00 (102/153): lz4-libs-1.9.4-4.fc39.ppc64le.rpm 2.3 MB/s | 85 kB 00:00 (103/153): ncurses-base-6.4-9.20240113.fc40.noa 2.5 MB/s | 63 kB 00:00 (104/153): mpfr-4.2.1-1.fc40.ppc64le.rpm 4.0 MB/s | 353 kB 00:00 (105/153): ncurses-libs-6.4-9.20240113.fc40.ppc 11 MB/s | 378 kB 00:00 (106/153): libxml2-2.12.4-1.fc40.ppc64le.rpm 3.9 MB/s | 765 kB 00:00 (107/153): ocaml-srpm-macros-9-1.fc40.noarch.rp 315 kB/s | 9.0 kB 00:00 (108/153): openblas-srpm-macros-2-14.fc39.noarc 265 kB/s | 7.5 kB 00:00 (109/153): openldap-2.6.6-1.fc39.ppc64le.rpm 3.7 MB/s | 287 kB 00:00 (110/153): openssl-libs-3.1.4-1.fc40.ppc64le.rp 19 MB/s | 2.3 MB 00:00 (111/153): p11-kit-0.25.3-1.fc40.ppc64le.rpm 4.0 MB/s | 507 kB 00:00 (112/153): p11-kit-trust-0.25.3-1.fc40.ppc64le. 2.8 MB/s | 157 kB 00:00 (113/153): package-notes-srpm-macros-0.5-9.fc39 288 kB/s | 11 kB 00:00 (114/153): pam-libs-1.6.0-1.fc40.ppc64le.rpm 1.8 MB/s | 63 kB 00:00 (115/153): pam-1.6.0-1.fc40.ppc64le.rpm 10 MB/s | 562 kB 00:00 (116/153): pcre2-10.42-2.fc40.ppc64le.rpm 8.0 MB/s | 241 kB 00:00 (117/153): perl-srpm-macros-1-51.fc39.noarch.rp 447 kB/s | 8.0 kB 00:00 (118/153): patch-2.7.6-22.fc39.ppc64le.rpm 2.5 MB/s | 137 kB 00:00 (119/153): pcre2-syntax-10.42-2.fc40.noarch.rpm 3.1 MB/s | 143 kB 00:00 (120/153): pkgconf-m4-1.9.5-2.fc39.noarch.rpm 588 kB/s | 14 kB 00:00 (121/153): pkgconf-1.9.5-2.fc39.ppc64le.rpm 1.4 MB/s | 43 kB 00:00 (122/153): pkgconf-pkg-config-1.9.5-2.fc39.ppc6 331 kB/s | 9.6 kB 00:00 (123/153): publicsuffix-list-dafsa-20240107-1.f 2.2 MB/s | 58 kB 00:00 (124/153): popt-1.19-3.fc39.ppc64le.rpm 1.9 MB/s | 64 kB 00:00 (125/153): pyproject-srpm-macros-1.12.0-1.fc40. 532 kB/s | 14 kB 00:00 (126/153): qt5-srpm-macros-5.15.12-1.fc40.noarc 435 kB/s | 8.4 kB 00:00 (127/153): python-srpm-macros-3.12-7.fc40.noarc 614 kB/s | 24 kB 00:00 (128/153): readline-8.2-7.fc40.ppc64le.rpm 10 MB/s | 230 kB 00:00 (129/153): qt6-srpm-macros-6.6.1-3.fc40.noarch. 187 kB/s | 8.8 kB 00:00 (130/153): redhat-rpm-config-280-1.fc40.noarch. 3.2 MB/s | 75 kB 00:00 (131/153): rpm-build-4.19.1-2.fc40.ppc64le.rpm 2.1 MB/s | 73 kB 00:00 (132/153): rpm-build-libs-4.19.1-2.fc40.ppc64le 3.6 MB/s | 103 kB 00:00 (133/153): rpm-libs-4.19.1-2.fc40.ppc64le.rpm 14 MB/s | 357 kB 00:00 (134/153): rust-srpm-macros-25.2-2.fc40.noarch. 373 kB/s | 13 kB 00:00 (135/153): rpm-4.19.1-2.fc40.ppc64le.rpm 4.0 MB/s | 511 kB 00:00 (136/153): sed-4.8-14.fc39.ppc64le.rpm 14 MB/s | 303 kB 00:00 (137/153): setup-2.14.5-1.fc40.noarch.rpm 2.9 MB/s | 148 kB 00:00 (138/153): shadow-utils-4.14.0-2.fc40.ppc64le.r 22 MB/s | 1.2 MB 00:00 (139/153): systemd-libs-255.3-1.fc40.ppc64le.rp 20 MB/s | 751 kB 00:00 (140/153): rpm-sequoia-1.6.0-1.fc40.ppc64le.rpm 8.5 MB/s | 1.5 MB 00:00 (141/153): unzip-6.0-62.fc39.ppc64le.rpm 4.4 MB/s | 190 kB 00:00 (142/153): tar-1.35-2.fc40.ppc64le.rpm 10 MB/s | 874 kB 00:00 (143/153): util-linux-2.39.3-4.fc40.ppc64le.rpm 15 MB/s | 1.2 MB 00:00 (144/153): which-2.21-40.fc39.ppc64le.rpm 2.3 MB/s | 43 kB 00:00 (145/153): xxhash-libs-0.8.2-1.fc39.ppc64le.rpm 2.0 MB/s | 37 kB 00:00 (146/153): xz-5.4.5-1.fc40.ppc64le.rpm 18 MB/s | 535 kB 00:00 (147/153): util-linux-core-2.39.3-4.fc40.ppc64l 4.6 MB/s | 533 kB 00:00 (148/153): xz-libs-5.4.5-1.fc40.ppc64le.rpm 6.2 MB/s | 121 kB 00:00 (149/153): zip-3.0-39.fc40.ppc64le.rpm 12 MB/s | 274 kB 00:00 (150/153): zig-srpm-macros-1-1.fc40.noarch.rpm 198 kB/s | 8.0 kB 00:00 (151/153): sqlite-libs-3.45.0-1.fc40.ppc64le.rp 2.7 MB/s | 817 kB 00:00 (152/153): zlib-ng-compat-2.1.6-1.fc40.ppc64le. 3.7 MB/s | 78 kB 00:00 (153/153): zstd-1.5.5-4.fc39.ppc64le.rpm 2.2 MB/s | 499 kB 00:00 -------------------------------------------------------------------------------- Total 13 MB/s | 56 MB 00:04 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.ppc64le 1/1 Preparing : 1/1 Installing : libgcc-14.0.1-0.3.fc40.ppc64le 1/153 Running scriptlet: libgcc-14.0.1-0.3.fc40.ppc64le 1/153 Installing : crypto-policies-20231204-1.git1e3a2e4.fc40.noarc 2/153 Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc40.noarc 2/153 Installing : fedora-release-identity-basic-40-0.29.noarch 3/153 Installing : fedora-repos-rawhide-40-0.2.noarch 4/153 Installing : fedora-gpg-keys-40-0.2.noarch 5/153 Installing : fedora-repos-40-0.2.noarch 6/153 Installing : fedora-release-common-40-0.29.noarch 7/153 Installing : fedora-release-40-0.29.noarch 8/153 Installing : setup-2.14.5-1.fc40.noarch 9/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-1.fc40.noarch 9/153 Installing : filesystem-3.18-6.fc39.ppc64le 10/153 Installing : basesystem-11-18.fc39.noarch 11/153 Installing : rust-srpm-macros-25.2-2.fc40.noarch 12/153 Installing : qt6-srpm-macros-6.6.1-3.fc40.noarch 13/153 Installing : qt5-srpm-macros-5.15.12-1.fc40.noarch 14/153 Installing : publicsuffix-list-dafsa-20240107-1.fc40.noarch 15/153 Installing : pkgconf-m4-1.9.5-2.fc39.noarch 16/153 Installing : perl-srpm-macros-1-51.fc39.noarch 17/153 Installing : pcre2-syntax-10.42-2.fc40.noarch 18/153 Installing : package-notes-srpm-macros-0.5-9.fc39.noarch 19/153 Installing : openblas-srpm-macros-2-14.fc39.noarch 20/153 Installing : ocaml-srpm-macros-9-1.fc40.noarch 21/153 Installing : ncurses-base-6.4-9.20240113.fc40.noarch 22/153 Installing : glibc-gconv-extra-2.38.9000-35.fc40.ppc64le 23/153 Running scriptlet: glibc-gconv-extra-2.38.9000-35.fc40.ppc64le 23/153 Installing : glibc-minimal-langpack-2.38.9000-35.fc40.ppc64le 24/153 Installing : glibc-common-2.38.9000-35.fc40.ppc64le 25/153 Running scriptlet: glibc-2.38.9000-35.fc40.ppc64le 26/153 Installing : glibc-2.38.9000-35.fc40.ppc64le 26/153 Running scriptlet: glibc-2.38.9000-35.fc40.ppc64le 26/153 Installing : ncurses-libs-6.4-9.20240113.fc40.ppc64le 27/153 Installing : bash-5.2.26-1.fc40.ppc64le 28/153 Running scriptlet: bash-5.2.26-1.fc40.ppc64le 28/153 Installing : zlib-ng-compat-2.1.6-1.fc40.ppc64le 29/153 Installing : xz-libs-5.4.5-1.fc40.ppc64le 30/153 Installing : bzip2-libs-1.0.8-16.fc39.ppc64le 31/153 Installing : readline-8.2-7.fc40.ppc64le 32/153 Installing : libstdc++-14.0.1-0.3.fc40.ppc64le 33/153 Installing : libuuid-2.39.3-4.fc40.ppc64le 34/153 Installing : libzstd-1.5.5-4.fc39.ppc64le 35/153 Installing : elfutils-libelf-0.190-4.fc40.ppc64le 36/153 Installing : popt-1.19-3.fc39.ppc64le 37/153 Installing : libblkid-2.39.3-4.fc40.ppc64le 38/153 Installing : gmp-1:6.2.1-5.fc39.ppc64le 39/153 Installing : libattr-2.5.2-1.fc40.ppc64le 40/153 Installing : libacl-2.3.2-1.fc40.ppc64le 41/153 Installing : libxcrypt-4.4.36-4.fc40.ppc64le 42/153 Installing : gdbm-libs-1:1.23-4.fc39.ppc64le 43/153 Installing : libeconf-0.5.2-1.fc40.ppc64le 44/153 Installing : lz4-libs-1.9.4-4.fc39.ppc64le 45/153 Installing : mpfr-4.2.1-1.fc40.ppc64le 46/153 Installing : gawk-5.3.0-1.fc40.ppc64le 47/153 Installing : dwz-0.15-3.fc39.ppc64le 48/153 Installing : unzip-6.0-62.fc39.ppc64le 49/153 Installing : file-libs-5.45-1.fc40.ppc64le 50/153 Installing : file-5.45-1.fc40.ppc64le 51/153 Installing : alternatives-1.26-1.fc40.ppc64le 52/153 Installing : jansson-2.13.1-7.fc39.ppc64le 53/153 Installing : libcap-ng-0.8.4-2.fc40.ppc64le 54/153 Installing : audit-libs-4.0-7.fc40.ppc64le 55/153 Installing : pam-libs-1.6.0-1.fc40.ppc64le 56/153 Installing : libcap-2.69-1.fc40.ppc64le 57/153 Installing : systemd-libs-255.3-1.fc40.ppc64le 58/153 Installing : libcom_err-1.47.0-2.fc39.ppc64le 59/153 Installing : libsepol-3.6-1.fc40.ppc64le 60/153 Installing : libsmartcols-2.39.3-4.fc40.ppc64le 61/153 Installing : libtasn1-4.19.0-3.fc39.ppc64le 62/153 Installing : libunistring-1.1-5.fc40.ppc64le 63/153 Installing : libidn2-2.3.4-3.fc39.ppc64le 64/153 Installing : lua-libs-5.4.6-3.fc39.ppc64le 65/153 Installing : pcre2-10.42-2.fc40.ppc64le 66/153 Installing : libselinux-3.6-2.fc40.ppc64le 67/153 Installing : sed-4.8-14.fc39.ppc64le 68/153 Installing : grep-3.11-5.fc40.ppc64le 69/153 Installing : findutils-1:4.9.0-6.fc40.ppc64le 70/153 Installing : xz-5.4.5-1.fc40.ppc64le 71/153 Installing : libmount-2.39.3-4.fc40.ppc64le 72/153 Installing : util-linux-core-2.39.3-4.fc40.ppc64le 73/153 Installing : libsemanage-3.6-1.fc40.ppc64le 74/153 Installing : shadow-utils-2:4.14.0-2.fc40.ppc64le 75/153 Running scriptlet: libutempter-1.2.1-10.fc39.ppc64le 76/153 Installing : libutempter-1.2.1-10.fc39.ppc64le 76/153 Installing : tar-2:1.35-2.fc40.ppc64le 77/153 Installing : libpsl-0.21.5-1.fc40.ppc64le 78/153 Installing : zip-3.0-39.fc40.ppc64le 79/153 Installing : zstd-1.5.5-4.fc39.ppc64le 80/153 Installing : cyrus-sasl-lib-2.1.28-17.fc40.ppc64le 81/153 Installing : gdbm-1:1.23-4.fc39.ppc64le 82/153 Installing : libfdisk-2.39.3-4.fc40.ppc64le 83/153 Installing : bzip2-1.0.8-16.fc39.ppc64le 84/153 Installing : libxml2-2.12.4-1.fc40.ppc64le 85/153 Installing : sqlite-libs-3.45.0-1.fc40.ppc64le 86/153 Installing : ed-1.20-1.fc40.ppc64le 87/153 Installing : patch-2.7.6-22.fc39.ppc64le 88/153 Installing : elfutils-default-yama-scope-0.190-4.fc40.noarch 89/153 Running scriptlet: elfutils-default-yama-scope-0.190-4.fc40.noarch 89/153 Installing : cpio-2.15-1.fc40.ppc64le 90/153 Installing : diffutils-3.10-3.fc39.ppc64le 91/153 Installing : keyutils-libs-1.6.3-1.fc40.ppc64le 92/153 Installing : libbrotli-1.1.0-1.fc40.ppc64le 93/153 Installing : libffi-3.4.4-5.fc40.ppc64le 94/153 Installing : p11-kit-0.25.3-1.fc40.ppc64le 95/153 Installing : p11-kit-trust-0.25.3-1.fc40.ppc64le 96/153 Running scriptlet: p11-kit-trust-0.25.3-1.fc40.ppc64le 96/153 Installing : libgomp-14.0.1-0.3.fc40.ppc64le 97/153 Installing : libnghttp2-1.59.0-1.fc40.ppc64le 98/153 Installing : libpkgconf-1.9.5-2.fc39.ppc64le 99/153 Installing : pkgconf-1.9.5-2.fc39.ppc64le 100/153 Installing : pkgconf-pkg-config-1.9.5-2.fc39.ppc64le 101/153 Installing : librtas-2.0.4-3.fc39.ppc64le 102/153 Running scriptlet: librtas-2.0.4-3.fc39.ppc64le 102/153 Installing : libverto-0.3.2-6.fc39.ppc64le 103/153 Installing : xxhash-libs-0.8.2-1.fc39.ppc64le 104/153 Installing : libssh-config-0.10.6-2.fc40.noarch 105/153 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 106/153 Installing : gnat-srpm-macros-6-3.fc39.noarch 107/153 Installing : ghc-srpm-macros-1.6.1-3.fc40.noarch 108/153 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 109/153 Installing : coreutils-common-9.4-3.fc40.ppc64le 110/153 Installing : openssl-libs-1:3.1.4-1.fc40.ppc64le 111/153 Installing : coreutils-9.4-3.fc40.ppc64le 112/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/153 Installing : ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/153 Installing : krb5-libs-1.21.2-3.fc40.ppc64le 114/153 Installing : libtirpc-1.3.4-1.rc1.fc40.ppc64le 115/153 Running scriptlet: authselect-libs-1.5.0-1.fc40.ppc64le 116/153 Installing : authselect-libs-1.5.0-1.fc40.ppc64le 116/153 Installing : gzip-1.12-6.fc39.ppc64le 117/153 Installing : cracklib-2.9.11-2.fc39.ppc64le 118/153 Installing : libpwquality-1.4.5-6.fc39.ppc64le 119/153 Installing : authselect-1.5.0-1.fc40.ppc64le 120/153 Installing : libnsl2-2.0.1-1.fc40.ppc64le 121/153 Installing : pam-1.6.0-1.fc40.ppc64le 122/153 Installing : libssh-0.10.6-2.fc40.ppc64le 123/153 Installing : libarchive-3.7.2-1.fc40.ppc64le 124/153 Installing : libevent-2.1.12-9.fc39.ppc64le 125/153 Installing : openldap-2.6.6-1.fc39.ppc64le 126/153 Installing : libcurl-8.5.0-2.fc40.ppc64le 127/153 Installing : elfutils-libs-0.190-4.fc40.ppc64le 128/153 Installing : elfutils-debuginfod-client-0.190-4.fc40.ppc64le 129/153 Installing : binutils-gold-2.41-30.fc40.ppc64le 130/153 Running scriptlet: binutils-gold-2.41-30.fc40.ppc64le 130/153 Installing : binutils-2.41-30.fc40.ppc64le 131/153 Running scriptlet: binutils-2.41-30.fc40.ppc64le 131/153 Installing : gdb-minimal-14.1-7.fc40.ppc64le 132/153 Installing : elfutils-0.190-4.fc40.ppc64le 133/153 Installing : debugedit-5.0-12.fc40.ppc64le 134/153 Installing : curl-8.5.0-2.fc40.ppc64le 135/153 Installing : rpm-sequoia-1.6.0-1.fc40.ppc64le 136/153 Installing : rpm-libs-4.19.1-2.fc40.ppc64le 137/153 Running scriptlet: rpm-4.19.1-2.fc40.ppc64le 138/153 Installing : rpm-4.19.1-2.fc40.ppc64le 138/153 Installing : efi-srpm-macros-5-9.fc39.noarch 139/153 Installing : lua-srpm-macros-1-9.fc39.noarch 140/153 Installing : zig-srpm-macros-1-1.fc40.noarch 141/153 Installing : rpm-build-libs-4.19.1-2.fc40.ppc64le 142/153 Installing : ansible-srpm-macros-1-12.fc40.noarch 143/153 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 144/153 Installing : forge-srpm-macros-0.2.0-1.fc40.noarch 145/153 Installing : go-srpm-macros-3.3.1-1.fc40.noarch 146/153 Installing : python-srpm-macros-3.12-7.fc40.noarch 147/153 Installing : redhat-rpm-config-280-1.fc40.noarch 148/153 Installing : rpm-build-4.19.1-2.fc40.ppc64le 149/153 Installing : pyproject-srpm-macros-1.12.0-1.fc40.noarch 150/153 Installing : util-linux-2.39.3-4.fc40.ppc64le 151/153 Installing : which-2.21-40.fc39.ppc64le 152/153 Installing : info-7.1-1.fc40.ppc64le 153/153 Running scriptlet: filesystem-3.18-6.fc39.ppc64le 153/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.5.0-1.fc40.ppc64le 153/153 Running scriptlet: rpm-4.19.1-2.fc40.ppc64le 153/153 Running scriptlet: info-7.1-1.fc40.ppc64le 153/153 Installed: alternatives-1.26-1.fc40.ppc64le ansible-srpm-macros-1-12.fc40.noarch audit-libs-4.0-7.fc40.ppc64le authselect-1.5.0-1.fc40.ppc64le authselect-libs-1.5.0-1.fc40.ppc64le basesystem-11-18.fc39.noarch bash-5.2.26-1.fc40.ppc64le binutils-2.41-30.fc40.ppc64le binutils-gold-2.41-30.fc40.ppc64le bzip2-1.0.8-16.fc39.ppc64le bzip2-libs-1.0.8-16.fc39.ppc64le ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-3.fc40.ppc64le coreutils-common-9.4-3.fc40.ppc64le cpio-2.15-1.fc40.ppc64le cracklib-2.9.11-2.fc39.ppc64le crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-2.fc40.ppc64le cyrus-sasl-lib-2.1.28-17.fc40.ppc64le debugedit-5.0-12.fc40.ppc64le diffutils-3.10-3.fc39.ppc64le dwz-0.15-3.fc39.ppc64le ed-1.20-1.fc40.ppc64le efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.ppc64le elfutils-debuginfod-client-0.190-4.fc40.ppc64le elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.ppc64le elfutils-libs-0.190-4.fc40.ppc64le fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.ppc64le file-libs-5.45-1.fc40.ppc64le filesystem-3.18-6.fc39.ppc64le findutils-1:4.9.0-6.fc40.ppc64le fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.3.0-1.fc40.ppc64le gdb-minimal-14.1-7.fc40.ppc64le gdbm-1:1.23-4.fc39.ppc64le gdbm-libs-1:1.23-4.fc39.ppc64le ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-35.fc40.ppc64le glibc-common-2.38.9000-35.fc40.ppc64le glibc-gconv-extra-2.38.9000-35.fc40.ppc64le glibc-minimal-langpack-2.38.9000-35.fc40.ppc64le gmp-1:6.2.1-5.fc39.ppc64le gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.ppc64le gzip-1.12-6.fc39.ppc64le info-7.1-1.fc40.ppc64le jansson-2.13.1-7.fc39.ppc64le kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc40.ppc64le krb5-libs-1.21.2-3.fc40.ppc64le libacl-2.3.2-1.fc40.ppc64le libarchive-3.7.2-1.fc40.ppc64le libattr-2.5.2-1.fc40.ppc64le libblkid-2.39.3-4.fc40.ppc64le libbrotli-1.1.0-1.fc40.ppc64le libcap-2.69-1.fc40.ppc64le libcap-ng-0.8.4-2.fc40.ppc64le libcom_err-1.47.0-2.fc39.ppc64le libcurl-8.5.0-2.fc40.ppc64le libeconf-0.5.2-1.fc40.ppc64le libevent-2.1.12-9.fc39.ppc64le libfdisk-2.39.3-4.fc40.ppc64le libffi-3.4.4-5.fc40.ppc64le libgcc-14.0.1-0.3.fc40.ppc64le libgomp-14.0.1-0.3.fc40.ppc64le libidn2-2.3.4-3.fc39.ppc64le libmount-2.39.3-4.fc40.ppc64le libnghttp2-1.59.0-1.fc40.ppc64le libnsl2-2.0.1-1.fc40.ppc64le libpkgconf-1.9.5-2.fc39.ppc64le libpsl-0.21.5-1.fc40.ppc64le libpwquality-1.4.5-6.fc39.ppc64le librtas-2.0.4-3.fc39.ppc64le libselinux-3.6-2.fc40.ppc64le libsemanage-3.6-1.fc40.ppc64le libsepol-3.6-1.fc40.ppc64le libsmartcols-2.39.3-4.fc40.ppc64le libssh-0.10.6-2.fc40.ppc64le libssh-config-0.10.6-2.fc40.noarch libstdc++-14.0.1-0.3.fc40.ppc64le libtasn1-4.19.0-3.fc39.ppc64le libtirpc-1.3.4-1.rc1.fc40.ppc64le libunistring-1.1-5.fc40.ppc64le libutempter-1.2.1-10.fc39.ppc64le libuuid-2.39.3-4.fc40.ppc64le libverto-0.3.2-6.fc39.ppc64le libxcrypt-4.4.36-4.fc40.ppc64le libxml2-2.12.4-1.fc40.ppc64le libzstd-1.5.5-4.fc39.ppc64le lua-libs-5.4.6-3.fc39.ppc64le lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.ppc64le mpfr-4.2.1-1.fc40.ppc64le ncurses-base-6.4-9.20240113.fc40.noarch ncurses-libs-6.4-9.20240113.fc40.ppc64le ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.ppc64le openssl-libs-1:3.1.4-1.fc40.ppc64le p11-kit-0.25.3-1.fc40.ppc64le p11-kit-trust-0.25.3-1.fc40.ppc64le package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.6.0-1.fc40.ppc64le pam-libs-1.6.0-1.fc40.ppc64le patch-2.7.6-22.fc39.ppc64le pcre2-10.42-2.fc40.ppc64le pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.ppc64le pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.ppc64le popt-1.19-3.fc39.ppc64le publicsuffix-list-dafsa-20240107-1.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-7.fc40.noarch qt5-srpm-macros-5.15.12-1.fc40.noarch qt6-srpm-macros-6.6.1-3.fc40.noarch readline-8.2-7.fc40.ppc64le redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-2.fc40.ppc64le rpm-build-4.19.1-2.fc40.ppc64le rpm-build-libs-4.19.1-2.fc40.ppc64le rpm-libs-4.19.1-2.fc40.ppc64le rpm-sequoia-1.6.0-1.fc40.ppc64le rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.ppc64le setup-2.14.5-1.fc40.noarch shadow-utils-2:4.14.0-2.fc40.ppc64le sqlite-libs-3.45.0-1.fc40.ppc64le systemd-libs-255.3-1.fc40.ppc64le tar-2:1.35-2.fc40.ppc64le unzip-6.0-62.fc39.ppc64le util-linux-2.39.3-4.fc40.ppc64le util-linux-core-2.39.3-4.fc40.ppc64le which-2.21-40.fc39.ppc64le xxhash-libs-0.8.2-1.fc39.ppc64le xz-5.4.5-1.fc40.ppc64le xz-libs-5.4.5-1.fc40.ppc64le zig-srpm-macros-1-1.fc40.noarch zip-3.0-39.fc40.ppc64le zlib-ng-compat-2.1.6-1.fc40.ppc64le zstd-1.5.5-4.fc39.ppc64le Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.26-1.fc40.ppc64le ansible-srpm-macros-1-12.fc40.noarch audit-libs-4.0-7.fc40.ppc64le authselect-1.5.0-1.fc40.ppc64le authselect-libs-1.5.0-1.fc40.ppc64le basesystem-11-18.fc39.noarch bash-5.2.26-1.fc40.ppc64le binutils-2.41-30.fc40.ppc64le binutils-gold-2.41-30.fc40.ppc64le bzip2-1.0.8-16.fc39.ppc64le bzip2-libs-1.0.8-16.fc39.ppc64le ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-3.fc40.ppc64le coreutils-common-9.4-3.fc40.ppc64le cpio-2.15-1.fc40.ppc64le cracklib-2.9.11-2.fc39.ppc64le crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-2.fc40.ppc64le cyrus-sasl-lib-2.1.28-17.fc40.ppc64le debugedit-5.0-12.fc40.ppc64le diffutils-3.10-3.fc39.ppc64le dwz-0.15-3.fc39.ppc64le ed-1.20-1.fc40.ppc64le efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.ppc64le elfutils-debuginfod-client-0.190-4.fc40.ppc64le elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.ppc64le elfutils-libs-0.190-4.fc40.ppc64le fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.ppc64le file-libs-5.45-1.fc40.ppc64le filesystem-3.18-6.fc39.ppc64le findutils-4.9.0-6.fc40.ppc64le fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.3.0-1.fc40.ppc64le gdb-minimal-14.1-7.fc40.ppc64le gdbm-1.23-4.fc39.ppc64le gdbm-libs-1.23-4.fc39.ppc64le ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-35.fc40.ppc64le glibc-common-2.38.9000-35.fc40.ppc64le glibc-gconv-extra-2.38.9000-35.fc40.ppc64le glibc-minimal-langpack-2.38.9000-35.fc40.ppc64le gmp-6.2.1-5.fc39.ppc64le gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.ppc64le gzip-1.12-6.fc39.ppc64le info-7.1-1.fc40.ppc64le jansson-2.13.1-7.fc39.ppc64le kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc40.ppc64le krb5-libs-1.21.2-3.fc40.ppc64le libacl-2.3.2-1.fc40.ppc64le libarchive-3.7.2-1.fc40.ppc64le libattr-2.5.2-1.fc40.ppc64le libblkid-2.39.3-4.fc40.ppc64le libbrotli-1.1.0-1.fc40.ppc64le libcap-2.69-1.fc40.ppc64le libcap-ng-0.8.4-2.fc40.ppc64le libcom_err-1.47.0-2.fc39.ppc64le libcurl-8.5.0-2.fc40.ppc64le libeconf-0.5.2-1.fc40.ppc64le libevent-2.1.12-9.fc39.ppc64le libfdisk-2.39.3-4.fc40.ppc64le libffi-3.4.4-5.fc40.ppc64le libgcc-14.0.1-0.3.fc40.ppc64le libgomp-14.0.1-0.3.fc40.ppc64le libidn2-2.3.4-3.fc39.ppc64le libmount-2.39.3-4.fc40.ppc64le libnghttp2-1.59.0-1.fc40.ppc64le libnsl2-2.0.1-1.fc40.ppc64le libpkgconf-1.9.5-2.fc39.ppc64le libpsl-0.21.5-1.fc40.ppc64le libpwquality-1.4.5-6.fc39.ppc64le librtas-2.0.4-3.fc39.ppc64le libselinux-3.6-2.fc40.ppc64le libsemanage-3.6-1.fc40.ppc64le libsepol-3.6-1.fc40.ppc64le libsmartcols-2.39.3-4.fc40.ppc64le libssh-0.10.6-2.fc40.ppc64le libssh-config-0.10.6-2.fc40.noarch libstdc++-14.0.1-0.3.fc40.ppc64le libtasn1-4.19.0-3.fc39.ppc64le libtirpc-1.3.4-1.rc1.fc40.ppc64le libunistring-1.1-5.fc40.ppc64le libutempter-1.2.1-10.fc39.ppc64le libuuid-2.39.3-4.fc40.ppc64le libverto-0.3.2-6.fc39.ppc64le libxcrypt-4.4.36-4.fc40.ppc64le libxml2-2.12.4-1.fc40.ppc64le libzstd-1.5.5-4.fc39.ppc64le lua-libs-5.4.6-3.fc39.ppc64le lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.ppc64le mpfr-4.2.1-1.fc40.ppc64le ncurses-base-6.4-9.20240113.fc40.noarch ncurses-libs-6.4-9.20240113.fc40.ppc64le ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.ppc64le openssl-libs-3.1.4-1.fc40.ppc64le p11-kit-0.25.3-1.fc40.ppc64le p11-kit-trust-0.25.3-1.fc40.ppc64le package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.6.0-1.fc40.ppc64le pam-libs-1.6.0-1.fc40.ppc64le patch-2.7.6-22.fc39.ppc64le pcre2-10.42-2.fc40.ppc64le pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.ppc64le pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.ppc64le popt-1.19-3.fc39.ppc64le publicsuffix-list-dafsa-20240107-1.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-7.fc40.noarch qt5-srpm-macros-5.15.12-1.fc40.noarch qt6-srpm-macros-6.6.1-3.fc40.noarch readline-8.2-7.fc40.ppc64le redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-2.fc40.ppc64le rpm-build-4.19.1-2.fc40.ppc64le rpm-build-libs-4.19.1-2.fc40.ppc64le rpm-libs-4.19.1-2.fc40.ppc64le rpm-sequoia-1.6.0-1.fc40.ppc64le rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.ppc64le setup-2.14.5-1.fc40.noarch shadow-utils-4.14.0-2.fc40.ppc64le sqlite-libs-3.45.0-1.fc40.ppc64le systemd-libs-255.3-1.fc40.ppc64le tar-1.35-2.fc40.ppc64le unzip-6.0-62.fc39.ppc64le util-linux-2.39.3-4.fc40.ppc64le util-linux-core-2.39.3-4.fc40.ppc64le which-2.21-40.fc39.ppc64le xxhash-libs-0.8.2-1.fc39.ppc64le xz-5.4.5-1.fc40.ppc64le xz-libs-5.4.5-1.fc40.ppc64le zig-srpm-macros-1-1.fc40.noarch zip-3.0-39.fc40.ppc64le zlib-ng-compat-2.1.6-1.fc40.ppc64le zstd-1.5.5-4.fc39.ppc64le Start: buildsrpm Start: rpmbuild -bs warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1706313600 Wrote: /builddir/build/SRPMS/seqan-1.4.2-53.fc40.src.rpm RPM build warnings: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-ylqm2bdy/seqan/seqan.spec) Config(child) 4 minutes 59 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/seqan-1.4.2-53.fc40.src.rpm) Config(fedora-39-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-ppc64le-bootstrap-1706322988.398155/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-ppc64le-bootstrap-1706322988.398155/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.ppc64le rpm-sequoia-1.5.0-1.fc39.ppc64le python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Finish: chroot init Start: build phase for seqan-1.4.2-53.fc40.src.rpm Start: build setup for seqan-1.4.2-53.fc40.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1706313600 warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Wrote: /builddir/build/SRPMS/seqan-1.4.2-53.fc40.src.rpm RPM build warnings: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 19 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 19 kB/s | 3.8 kB 00:00 fedora 44 kB/s | 3.8 kB 00:00 updates 70 kB/s | 4.9 kB 00:00 updates 392 kB/s | 453 kB 00:01 Last metadata expiration check: 0:00:01 ago on Sat Jan 27 02:41:51 2024. Dependencies resolved. ============================================================================================================================================= Package Arch Version Repository Size ============================================================================================================================================= Installing: boost-devel ppc64le 1.83.0-2.fc40 copr_base 12 M bzip2-devel ppc64le 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 214 k cmake ppc64le 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 M coin-or-lemon-devel ppc64le 1.3.1-29.fc40 copr_base 287 k gcc ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 M gcc-c++ ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 M java-1.8.0-openjdk-devel ppc64le 1:1.8.0.392.b08-7.fc39 updates 7.4 M libstdc++-static ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M llvm-devel ppc64le 17.0.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.6 M make ppc64le 1:4.4.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 597 k python3-devel ppc64le 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274 k python3-setuptools noarch 68.2.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M qt-devel ppc64le 1:4.8.7-74.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.8 M zlib-ng-compat-devel ppc64le 2.1.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36 k Installing dependencies: Lmod ppc64le 8.7.32-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 234 k MUMPS ppc64le 5.6.2-3.fc40 copr_base 2.0 M MUMPS-common noarch 5.6.2-3.fc40 copr_base 883 k abattis-cantarell-vf-fonts noarch 0.301-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k alsa-lib ppc64le 1.2.10-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 577 k annobin-docs noarch 12.38-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 90 k annobin-plugin-gcc ppc64le 12.38-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 959 k avahi-libs ppc64le 0.8-24.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72 k boost ppc64le 1.83.0-2.fc40 copr_base 14 k boost-atomic ppc64le 1.83.0-2.fc40 copr_base 20 k boost-chrono ppc64le 1.83.0-2.fc40 copr_base 26 k boost-container ppc64le 1.83.0-2.fc40 copr_base 42 k boost-context ppc64le 1.83.0-2.fc40 copr_base 18 k boost-contract ppc64le 1.83.0-2.fc40 copr_base 46 k boost-coroutine ppc64le 1.83.0-2.fc40 copr_base 21 k boost-date-time ppc64le 1.83.0-2.fc40 copr_base 16 k boost-fiber ppc64le 1.83.0-2.fc40 copr_base 45 k boost-filesystem ppc64le 1.83.0-2.fc40 copr_base 70 k boost-graph ppc64le 1.83.0-2.fc40 copr_base 156 k boost-iostreams ppc64le 1.83.0-2.fc40 copr_base 41 k boost-json ppc64le 1.83.0-2.fc40 copr_base 153 k boost-locale ppc64le 1.83.0-2.fc40 copr_base 235 k boost-log ppc64le 1.83.0-2.fc40 copr_base 514 k boost-math ppc64le 1.83.0-2.fc40 copr_base 316 k boost-nowide ppc64le 1.83.0-2.fc40 copr_base 22 k boost-numpy3 ppc64le 1.83.0-2.fc40 copr_base 30 k boost-program-options ppc64le 1.83.0-2.fc40 copr_base 113 k boost-python3 ppc64le 1.83.0-2.fc40 copr_base 118 k boost-random ppc64le 1.83.0-2.fc40 copr_base 25 k boost-regex ppc64le 1.83.0-2.fc40 copr_base 121 k boost-serialization ppc64le 1.83.0-2.fc40 copr_base 139 k boost-stacktrace ppc64le 1.83.0-2.fc40 copr_base 31 k boost-system ppc64le 1.83.0-2.fc40 copr_base 16 k boost-test ppc64le 1.83.0-2.fc40 copr_base 247 k boost-thread ppc64le 1.83.0-2.fc40 copr_base 64 k boost-timer ppc64le 1.83.0-2.fc40 copr_base 42 k boost-type_erasure ppc64le 1.83.0-2.fc40 copr_base 34 k boost-wave ppc64le 1.83.0-2.fc40 copr_base 218 k brotli ppc64le 1.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 20 k brotli-devel ppc64le 1.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k byte-buddy noarch 1.14.2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.2 M byte-buddy-agent noarch 1.14.2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 215 k cairo ppc64le 1.18.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 796 k cliquer-libs ppc64le 1.22-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k cmake-data noarch 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 M cmake-filesystem ppc64le 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k cmake-rpm-macros noarch 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k coin-or-Cbc ppc64le 2.10.5-16.fc40 copr_base 857 k coin-or-Cgl ppc64le 0.60.3-12.fc40 copr_base 449 k coin-or-Clp ppc64le 1.17.6-17.fc40 copr_base 1.0 M coin-or-CoinUtils ppc64le 2.11.4-12.fc40 copr_base 531 k coin-or-Osi ppc64le 0.108.6-11.fc40 copr_base 325 k coin-or-lemon ppc64le 1.3.1-29.fc40 copr_base 85 k copy-jdk-configs noarch 4.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 k cpp ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10 M crypto-policies-scripts noarch 20231204-1.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 105 k cups-libs ppc64le 1:2.4.7-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 314 k dbus-libs ppc64le 1:1.14.10-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 177 k default-fonts-core-sans noarch 4.0-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k double-conversion ppc64le 3.3.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 55 k duktape ppc64le 2.7.0-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183 k emacs-filesystem noarch 1:29.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.6 k expat ppc64le 2.5.0-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 116 k flexiblas ppc64le 3.4.1-3.fc40 copr_base 25 k flexiblas-netlib ppc64le 3.4.1-3.fc40 copr_base 2.9 M flexiblas-openblas-openmp ppc64le 3.4.1-3.fc40 copr_base 17 k fontconfig ppc64le 2.15.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 301 k fontconfig-devel ppc64le 2.15.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 129 k fonts-filesystem noarch 1:2.0.5-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.2 k freetype ppc64le 2.13.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 468 k freetype-devel ppc64le 2.13.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 913 k gc ppc64le 8.2.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 122 k gcc-plugin-annobin ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k gecode ppc64le 6.2.0-13.fc39 copr_base 3.2 M gettext ppc64le 0.22-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M gettext-envsubst ppc64le 0.22-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k gettext-libs ppc64le 0.22-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 375 k gettext-runtime ppc64le 0.22-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 111 k gl-manpages noarch 1.1-29.20190306.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M glib2 ppc64le 2.79.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.1 M glib2-devel ppc64le 2.79.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 M glibc-devel ppc64le 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 541 k glpk ppc64le 5.0-10.fc40 copr_base 414 k glx-utils ppc64le 9.0.0-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 74 k gnutls ppc64le 3.8.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M google-noto-fonts-common noarch 20230801-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17 k google-noto-sans-vf-fonts noarch 20230801-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 583 k graphite2 ppc64le 1.3.14-13.fc40 copr_base 105 k graphite2-devel ppc64le 1.3.14-13.fc40 copr_base 21 k gsl ppc64le 2.7.1-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M guile22 ppc64le 2.2.7-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.5 M hamcrest noarch 2.2-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 120 k harfbuzz ppc64le 8.3.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M harfbuzz-devel ppc64le 8.3.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 419 k harfbuzz-icu ppc64le 8.3.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17 k jacop noarch 4.9.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 M java-1.8.0-openjdk ppc64le 1:1.8.0.392.b08-7.fc39 updates 487 k java-1.8.0-openjdk-headless ppc64le 1:1.8.0.392.b08-7.fc39 updates 33 M java-17-openjdk-headless ppc64le 1:17.0.10.0.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 44 M javapackages-filesystem noarch 6.2.0-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k javapackages-tools noarch 6.2.0-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 33 k jbigkit-libs ppc64le 2.1-27.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 56 k jsoncpp ppc64le 1.9.5-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 99 k junit noarch 1:4.13.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 347 k kernel-headers ppc64le 6.8.0-0.rc1.12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M lcms2 ppc64le 2.16-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 207 k libICE ppc64le 1.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 81 k libICE-devel ppc64le 1.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 46 k libSM ppc64le 1.2.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 44 k libSM-devel ppc64le 1.2.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k libX11 ppc64le 1.8.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 699 k libX11-common noarch 1.8.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144 k libX11-devel ppc64le 1.8.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 912 k libX11-xcb ppc64le 1.8.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k libXau ppc64le 1.0.11-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k libXau-devel ppc64le 1.0.11-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k libXcomposite ppc64le 0.4.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k libXcursor ppc64le 1.2.1-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k libXcursor-devel ppc64le 1.2.1-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29 k libXext ppc64le 1.3.5-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k libXext-devel ppc64le 1.3.5-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72 k libXfixes ppc64le 6.0.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k libXfixes-devel ppc64le 6.0.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k libXft ppc64le 2.3.8-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 78 k libXft-devel ppc64le 2.3.8-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36 k libXi ppc64le 1.8.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k libXi-devel ppc64le 1.8.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103 k libXinerama ppc64le 1.1.5-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k libXinerama-devel ppc64le 1.1.5-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k libXrandr ppc64le 1.5.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 k libXrandr-devel ppc64le 1.5.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k libXrender ppc64le 0.9.11-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29 k libXrender-devel ppc64le 0.9.11-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k libXt ppc64le 1.3.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197 k libXt-devel ppc64le 1.3.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 408 k libXtst ppc64le 1.2.4-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k libXv ppc64le 1.0.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k libXv-devel ppc64le 1.0.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k libXxf86vm ppc64le 1.1.5-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k libasan ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 498 k libatomic ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k libb2 ppc64le 0.98.1-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k libblkid-devel ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k libdrm ppc64le 2.4.120-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 110 k libedit ppc64le 3.1-48.20230828cvs.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k libedit-devel ppc64le 3.1-48.20230828cvs.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k libevdev ppc64le 1.13.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 44 k libffi-devel ppc64le 3.4.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 k libfontenc ppc64le 1.1.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 33 k libgfortran ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 613 k libglvnd ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 131 k libglvnd-core-devel ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17 k libglvnd-devel ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 157 k libglvnd-egl ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k libglvnd-gles ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k libglvnd-glx ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 148 k libglvnd-opengl ppc64le 1:1.7.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k libgudev ppc64le 238-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k libicu ppc64le 73.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 M libicu-devel ppc64le 73.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 850 k libinput ppc64le 1.25.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 220 k libjpeg-turbo ppc64le 2.1.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 208 k liblerc ppc64le 4.0.0-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 220 k libmng ppc64le 2.0.3-19.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 206 k libmount-devel ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k libmpc ppc64le 1.3.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 95 k libnauty ppc64le 2.8.8-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 942 k libpng ppc64le 2:1.6.40-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 137 k libpng-devel ppc64le 2:1.6.40-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 294 k libproxy ppc64le 0.5.3-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 50 k libquadmath ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 199 k libselinux-devel ppc64le 3.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 115 k libsepol-devel ppc64le 3.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k libstdc++-devel ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.6 M libtiff ppc64le 4.5.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 343 k libtool-ltdl ppc64le 2.4.7-10.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k libubsan ppc64le 14.0.1-0.3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 244 k libuuid-devel ppc64le 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k libuv ppc64le 1:1.47.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 260 k libwacom ppc64le 2.9.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 47 k libwacom-data noarch 2.9.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 118 k libwayland-client ppc64le 1.22.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36 k libwayland-server ppc64le 1.22.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 46 k libwebp ppc64le 1.3.2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 269 k libxcb ppc64le 1.16-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 251 k libxcb-devel ppc64le 1.16-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M libxcrypt-devel ppc64le 4.4.36-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29 k libxkbcommon ppc64le 1.6.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 154 k libxkbcommon-x11 ppc64le 1.6.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k libxml2-devel ppc64le 2.12.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 495 k libxshmfence ppc64le 1.3.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k lksctp-tools ppc64le 1.0.19-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96 k llvm ppc64le 17.0.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26 M llvm-googletest ppc64le 17.0.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 368 k llvm-libs ppc64le 17.0.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 M llvm-static ppc64le 17.0.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36 M llvm-test ppc64le 17.0.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 659 k lua ppc64le 5.4.6-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 201 k lua-filesystem ppc64le 1.8.0-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k lua-json noarch 1.3.4-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26 k lua-lpeg ppc64le 1.0.2-11.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 70 k lua-posix ppc64le 36.2.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 143 k lua-term ppc64le 0.08-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 16 k mesa-libEGL ppc64le 24.0.0~rc2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 150 k mesa-libGL ppc64le 24.0.0~rc2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197 k mesa-libGLU ppc64le 9.0.3-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 178 k mesa-libGLU-devel ppc64le 9.0.3-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k mesa-libgbm ppc64le 24.0.0~rc2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k mesa-libglapi ppc64le 24.0.0~rc2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k metis ppc64le 5.1.0.3-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 598 k mkfontscale ppc64le 1.2.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 k mockito noarch 5.8.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 592 k mp ppc64le 3.1.0-42.20200303git7fd4828.fc39 copr_base 1.0 M mpdecimal ppc64le 2.5.1-7.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 104 k mtdev ppc64le 1.1.6-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k ncurses-c++-libs ppc64le 6.4-9.20240113.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k ncurses-devel ppc64le 6.4-9.20240113.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 535 k nettle ppc64le 3.9.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 460 k nspr ppc64le 4.35.0-17.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 172 k nss ppc64le 3.96.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 790 k nss-softokn ppc64le 3.96.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 440 k nss-softokn-freebl ppc64le 3.96.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 369 k nss-sysinit ppc64le 3.96.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k nss-util ppc64le 3.96.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 97 k objectweb-asm noarch 9.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 362 k objenesis noarch 3.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 115 k openblas ppc64le 0.3.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k openblas-openmp ppc64le 0.3.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.6 M opentest4j noarch 1.3.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26 k pcre2-devel ppc64le 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 473 k pcre2-utf16 ppc64le 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 220 k pcre2-utf32 ppc64le 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 207 k pixman ppc64le 0.43.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 230 k procps-ng ppc64le 4.0.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 391 k pyproject-rpm-macros noarch 1.12.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python-pip-wheel noarch 23.3.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 M python-rpm-macros noarch 3.12-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k python3 ppc64le 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k python3-libs ppc64le 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.0 M python3-numpy ppc64le 1:1.26.2-4.fc40 copr_base 6.8 M python3-packaging noarch 23.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 115 k python3-rpm-generators noarch 14-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 30 k python3-rpm-macros noarch 3.12-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k qt ppc64le 1:4.8.7-74.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.7 M qt-common noarch 1:4.8.7-74.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.7 k qt-settings noarch 39.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.8 k qt-x11 ppc64le 1:4.8.7-74.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 M qt5-qtbase ppc64le 5.15.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.8 M qt5-qtbase-common noarch 5.15.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k qt5-qtbase-gui ppc64le 5.15.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.0 M rhash ppc64le 1.4.3-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 206 k scotch ppc64le 7.0.4-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 341 k scotch-devel ppc64le 7.0.4-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k suitesparse ppc64le 5.13.0-4.fc40 copr_base 1.2 M sysprof-capture-devel ppc64le 45.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 62 k tcl ppc64le 1:8.6.13-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M ttmkfdir ppc64le 3.0.9-69.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 56 k tzdata noarch 2023d-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 434 k tzdata-java noarch 2023d-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 47 k unixODBC ppc64le 2.3.12-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 498 k vim-filesystem noarch 2:9.1.031-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17 k xcb-util ppc64le 0.4.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k xcb-util-image ppc64le 0.4.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 20 k xcb-util-keysyms ppc64le 0.4.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 15 k xcb-util-renderutil ppc64le 0.3.10-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k xcb-util-wm ppc64le 0.4.2-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k xkeyboard-config noarch 2.40-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 917 k xml-common noarch 0.6.3-62.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k xorg-x11-fonts-Type1 noarch 7.5-37.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 499 k xorg-x11-proto-devel noarch 2023.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 263 k xz-devel ppc64le 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 62 k Transaction Summary ============================================================================================================================================= Install 285 Packages Total download size: 411 M Installed size: 1.9 G Downloading Packages: (1/285): boost-1.83.0-2.fc40.ppc64le.rpm 148 kB/s | 14 kB 00:00 (2/285): boost-atomic-1.83.0-2.fc40.ppc64le.rpm 535 kB/s | 20 kB 00:00 (3/285): MUMPS-common-5.6.2-3.fc40.noarch.rpm 6.1 MB/s | 883 kB 00:00 (4/285): boost-chrono-1.83.0-2.fc40.ppc64le.rpm 905 kB/s | 26 kB 00:00 (5/285): MUMPS-5.6.2-3.fc40.ppc64le.rpm 11 MB/s | 2.0 MB 00:00 (6/285): boost-container-1.83.0-2.fc40.ppc64le. 1.2 MB/s | 42 kB 00:00 (7/285): boost-context-1.83.0-2.fc40.ppc64le.rp 1.5 MB/s | 18 kB 00:00 (8/285): boost-date-time-1.83.0-2.fc40.ppc64le. 1.2 MB/s | 16 kB 00:00 (9/285): boost-coroutine-1.83.0-2.fc40.ppc64le. 1.3 MB/s | 21 kB 00:00 (10/285): boost-contract-1.83.0-2.fc40.ppc64le. 2.5 MB/s | 46 kB 00:00 (11/285): boost-fiber-1.83.0-2.fc40.ppc64le.rpm 4.0 MB/s | 45 kB 00:00 (12/285): boost-filesystem-1.83.0-2.fc40.ppc64l 4.6 MB/s | 70 kB 00:00 (13/285): boost-graph-1.83.0-2.fc40.ppc64le.rpm 9.5 MB/s | 156 kB 00:00 (14/285): boost-iostreams-1.83.0-2.fc40.ppc64le 3.2 MB/s | 41 kB 00:00 (15/285): boost-json-1.83.0-2.fc40.ppc64le.rpm 5.5 MB/s | 153 kB 00:00 (16/285): boost-locale-1.83.0-2.fc40.ppc64le.rp 7.7 MB/s | 235 kB 00:00 (17/285): boost-log-1.83.0-2.fc40.ppc64le.rpm 7.5 MB/s | 514 kB 00:00 (18/285): boost-math-1.83.0-2.fc40.ppc64le.rpm 4.1 MB/s | 316 kB 00:00 (19/285): boost-nowide-1.83.0-2.fc40.ppc64le.rp 1.3 MB/s | 22 kB 00:00 (20/285): boost-numpy3-1.83.0-2.fc40.ppc64le.rp 2.5 MB/s | 30 kB 00:00 (21/285): boost-program-options-1.83.0-2.fc40.p 6.4 MB/s | 113 kB 00:00 (22/285): boost-python3-1.83.0-2.fc40.ppc64le.r 7.2 MB/s | 118 kB 00:00 (23/285): boost-random-1.83.0-2.fc40.ppc64le.rp 2.3 MB/s | 25 kB 00:00 (24/285): boost-regex-1.83.0-2.fc40.ppc64le.rpm 8.1 MB/s | 121 kB 00:00 (25/285): boost-serialization-1.83.0-2.fc40.ppc 9.8 MB/s | 139 kB 00:00 (26/285): boost-stacktrace-1.83.0-2.fc40.ppc64l 1.7 MB/s | 31 kB 00:00 (27/285): boost-system-1.83.0-2.fc40.ppc64le.rp 719 kB/s | 16 kB 00:00 (28/285): boost-test-1.83.0-2.fc40.ppc64le.rpm 7.8 MB/s | 247 kB 00:00 (29/285): boost-thread-1.83.0-2.fc40.ppc64le.rp 2.9 MB/s | 64 kB 00:00 (30/285): boost-timer-1.83.0-2.fc40.ppc64le.rpm 3.0 MB/s | 42 kB 00:00 (31/285): boost-type_erasure-1.83.0-2.fc40.ppc6 2.2 MB/s | 34 kB 00:00 (32/285): boost-wave-1.83.0-2.fc40.ppc64le.rpm 11 MB/s | 218 kB 00:00 (33/285): coin-or-Cbc-2.10.5-16.fc40.ppc64le.rp 22 MB/s | 857 kB 00:00 (34/285): coin-or-Cgl-0.60.3-12.fc40.ppc64le.rp 10 MB/s | 449 kB 00:00 (35/285): coin-or-CoinUtils-2.11.4-12.fc40.ppc6 12 MB/s | 531 kB 00:00 (36/285): coin-or-Clp-1.17.6-17.fc40.ppc64le.rp 14 MB/s | 1.0 MB 00:00 (37/285): coin-or-lemon-1.3.1-29.fc40.ppc64le.r 3.3 MB/s | 85 kB 00:00 (38/285): coin-or-Osi-0.108.6-11.fc40.ppc64le.r 8.4 MB/s | 325 kB 00:00 (39/285): flexiblas-3.4.1-3.fc40.ppc64le.rpm 1.4 MB/s | 25 kB 00:00 (40/285): boost-devel-1.83.0-2.fc40.ppc64le.rpm 25 MB/s | 12 MB 00:00 (41/285): coin-or-lemon-devel-1.3.1-29.fc40.ppc 2.8 MB/s | 287 kB 00:00 (42/285): flexiblas-netlib-3.4.1-3.fc40.ppc64le 29 MB/s | 2.9 MB 00:00 (43/285): flexiblas-openblas-openmp-3.4.1-3.fc4 581 kB/s | 17 kB 00:00 (44/285): graphite2-1.3.14-13.fc40.ppc64le.rpm 5.4 MB/s | 105 kB 00:00 (45/285): glpk-5.0-10.fc40.ppc64le.rpm 13 MB/s | 414 kB 00:00 (46/285): graphite2-devel-1.3.14-13.fc40.ppc64l 1.2 MB/s | 21 kB 00:00 (47/285): gecode-6.2.0-13.fc39.ppc64le.rpm 29 MB/s | 3.2 MB 00:00 (48/285): mp-3.1.0-42.20200303git7fd4828.fc39.p 17 MB/s | 1.0 MB 00:00 (49/285): suitesparse-5.13.0-4.fc40.ppc64le.rpm 28 MB/s | 1.2 MB 00:00 (50/285): Lmod-8.7.32-1.fc40.ppc64le.rpm 2.3 MB/s | 234 kB 00:00 (51/285): abattis-cantarell-vf-fonts-0.301-10.f 1.4 MB/s | 121 kB 00:00 (52/285): alsa-lib-1.2.10-3.fc40.ppc64le.rpm 18 MB/s | 577 kB 00:00 (53/285): annobin-docs-12.38-1.fc40.noarch.rpm 4.0 MB/s | 90 kB 00:00 (54/285): annobin-plugin-gcc-12.38-1.fc40.ppc64 27 MB/s | 959 kB 00:00 (55/285): avahi-libs-0.8-24.fc39.ppc64le.rpm 2.1 MB/s | 72 kB 00:00 (56/285): python3-numpy-1.26.2-4.fc40.ppc64le.r 26 MB/s | 6.8 MB 00:00 (57/285): brotli-1.1.0-1.fc40.ppc64le.rpm 524 kB/s | 20 kB 00:00 (58/285): brotli-devel-1.1.0-1.fc40.ppc64le.rpm 662 kB/s | 34 kB 00:00 (59/285): bzip2-devel-1.0.8-16.fc39.ppc64le.rpm 5.1 MB/s | 214 kB 00:00 (60/285): byte-buddy-1.14.2-4.fc40.noarch.rpm 36 MB/s | 3.2 MB 00:00 (61/285): byte-buddy-agent-1.14.2-4.fc40.noarch 2.3 MB/s | 215 kB 00:00 (62/285): cairo-1.18.0-1.fc40.ppc64le.rpm 20 MB/s | 796 kB 00:00 (63/285): cliquer-libs-1.22-6.fc39.ppc64le.rpm 1.8 MB/s | 42 kB 00:00 (64/285): cmake-data-3.27.7-1.fc40.noarch.rpm 24 MB/s | 1.7 MB 00:00 (65/285): cmake-filesystem-3.27.7-1.fc40.ppc64l 264 kB/s | 19 kB 00:00 (66/285): cmake-rpm-macros-3.27.7-1.fc40.noarch 796 kB/s | 19 kB 00:00 (67/285): copy-jdk-configs-4.1-3.fc39.noarch.rp 1.4 MB/s | 28 kB 00:00 (68/285): crypto-policies-scripts-20231204-1.gi 3.9 MB/s | 105 kB 00:00 (69/285): cmake-3.27.7-1.fc40.ppc64le.rpm 48 MB/s | 11 MB 00:00 (70/285): cups-libs-2.4.7-7.fc40.ppc64le.rpm 3.1 MB/s | 314 kB 00:00 (71/285): dbus-libs-1.14.10-1.fc40.ppc64le.rpm 2.2 MB/s | 177 kB 00:00 (72/285): default-fonts-core-sans-4.0-9.fc40.no 331 kB/s | 25 kB 00:00 (73/285): double-conversion-3.3.0-1.fc40.ppc64l 1.2 MB/s | 55 kB 00:00 (74/285): duktape-2.7.0-5.fc39.ppc64le.rpm 3.8 MB/s | 183 kB 00:00 (75/285): emacs-filesystem-29.2-2.fc40.noarch.r 107 kB/s | 7.6 kB 00:00 (76/285): expat-2.5.0-3.fc39.ppc64le.rpm 1.6 MB/s | 116 kB 00:00 (77/285): fontconfig-2.15.0-1.fc40.ppc64le.rpm 12 MB/s | 301 kB 00:00 (78/285): fontconfig-devel-2.15.0-1.fc40.ppc64l 4.9 MB/s | 129 kB 00:00 (79/285): fonts-filesystem-2.0.5-12.fc39.noarch 424 kB/s | 8.2 kB 00:00 (80/285): freetype-2.13.2-1.fc40.ppc64le.rpm 14 MB/s | 468 kB 00:00 (81/285): freetype-devel-2.13.2-1.fc40.ppc64le. 24 MB/s | 913 kB 00:00 (82/285): gc-8.2.2-4.fc39.ppc64le.rpm 4.8 MB/s | 122 kB 00:00 (83/285): cpp-14.0.1-0.3.fc40.ppc64le.rpm 20 MB/s | 10 MB 00:00 (84/285): gcc-plugin-annobin-14.0.1-0.3.fc40.pp 1.7 MB/s | 37 kB 00:00 (85/285): gettext-0.22-2.fc39.ppc64le.rpm 10 MB/s | 1.1 MB 00:00 (86/285): gettext-envsubst-0.22-2.fc39.ppc64le. 1.4 MB/s | 37 kB 00:00 (87/285): gettext-libs-0.22-2.fc39.ppc64le.rpm 11 MB/s | 375 kB 00:00 (88/285): gettext-runtime-0.22-2.fc39.ppc64le.r 2.2 MB/s | 111 kB 00:00 (89/285): gcc-c++-14.0.1-0.3.fc40.ppc64le.rpm 26 MB/s | 13 MB 00:00 (90/285): gl-manpages-1.1-29.20190306.fc40.noar 6.5 MB/s | 1.0 MB 00:00 (91/285): glib2-devel-2.79.1-1.fc40.ppc64le.rpm 15 MB/s | 1.3 MB 00:00 (92/285): glib2-2.79.1-1.fc40.ppc64le.rpm 26 MB/s | 3.1 MB 00:00 (93/285): glibc-devel-2.38.9000-35.fc40.ppc64le 11 MB/s | 541 kB 00:00 (94/285): glx-utils-9.0.0-4.fc40.ppc64le.rpm 2.3 MB/s | 74 kB 00:00 (95/285): google-noto-fonts-common-20230801-4.f 811 kB/s | 17 kB 00:00 (96/285): gnutls-3.8.3-2.fc40.ppc64le.rpm 20 MB/s | 1.1 MB 00:00 (97/285): google-noto-sans-vf-fonts-20230801-4. 21 MB/s | 583 kB 00:00 (98/285): gsl-2.7.1-5.fc39.ppc64le.rpm 26 MB/s | 1.2 MB 00:00 (99/285): hamcrest-2.2-12.fc40.noarch.rpm 4.7 MB/s | 120 kB 00:00 (100/285): harfbuzz-8.3.0-2.fc40.ppc64le.rpm 24 MB/s | 1.0 MB 00:00 (101/285): harfbuzz-devel-8.3.0-2.fc40.ppc64le. 14 MB/s | 419 kB 00:00 (102/285): harfbuzz-icu-8.3.0-2.fc40.ppc64le.rp 538 kB/s | 17 kB 00:00 (103/285): jacop-4.9.0-2.fc39.noarch.rpm 29 MB/s | 1.7 MB 00:00 (104/285): guile22-2.2.7-9.fc39.ppc64le.rpm 24 MB/s | 6.5 MB 00:00 (105/285): javapackages-filesystem-6.2.0-5.fc40 616 kB/s | 13 kB 00:00 (106/285): javapackages-tools-6.2.0-5.fc40.noar 1.6 MB/s | 33 kB 00:00 (107/285): jbigkit-libs-2.1-27.fc40.ppc64le.rpm 2.5 MB/s | 56 kB 00:00 (108/285): jsoncpp-1.9.5-5.fc39.ppc64le.rpm 4.4 MB/s | 99 kB 00:00 (109/285): junit-4.13.2-2.fc40.noarch.rpm 10 MB/s | 347 kB 00:00 (110/285): kernel-headers-6.8.0-0.rc1.12.fc40.p 20 MB/s | 1.4 MB 00:00 (111/285): lcms2-2.16-2.fc40.ppc64le.rpm 8.3 MB/s | 207 kB 00:00 (112/285): libICE-1.1.1-1.fc40.ppc64le.rpm 3.1 MB/s | 81 kB 00:00 (113/285): gcc-14.0.1-0.3.fc40.ppc64le.rpm 24 MB/s | 32 MB 00:01 (114/285): libICE-devel-1.1.1-1.fc40.ppc64le.rp 311 kB/s | 46 kB 00:00 (115/285): libSM-1.2.4-1.fc40.ppc64le.rpm 1.5 MB/s | 44 kB 00:00 (116/285): libSM-devel-1.2.4-1.fc40.ppc64le.rpm 294 kB/s | 12 kB 00:00 (117/285): libX11-1.8.7-1.fc40.ppc64le.rpm 13 MB/s | 699 kB 00:00 (118/285): libX11-common-1.8.7-1.fc40.noarch.rp 6.1 MB/s | 144 kB 00:00 (119/285): libX11-xcb-1.8.7-1.fc40.ppc64le.rpm 161 kB/s | 12 kB 00:00 (120/285): libX11-devel-1.8.7-1.fc40.ppc64le.rp 7.4 MB/s | 912 kB 00:00 (121/285): libXau-1.0.11-4.fc40.ppc64le.rpm 788 kB/s | 32 kB 00:00 (122/285): libXau-devel-1.0.11-4.fc40.ppc64le.r 365 kB/s | 13 kB 00:00 (123/285): libXcomposite-0.4.6-1.fc40.ppc64le.r 661 kB/s | 25 kB 00:00 (124/285): libXcursor-1.2.1-5.fc40.ppc64le.rpm 566 kB/s | 34 kB 00:00 (125/285): libXcursor-devel-1.2.1-5.fc40.ppc64l 479 kB/s | 29 kB 00:00 (126/285): libXext-1.3.5-5.fc40.ppc64le.rpm 1.1 MB/s | 41 kB 00:00 (127/285): libXext-devel-1.3.5-5.fc40.ppc64le.r 1.9 MB/s | 72 kB 00:00 (128/285): libXfixes-6.0.1-1.fc40.ppc64le.rpm 502 kB/s | 19 kB 00:00 (129/285): libXfixes-devel-6.0.1-1.fc40.ppc64le 318 kB/s | 12 kB 00:00 (130/285): libXft-2.3.8-4.fc40.ppc64le.rpm 1.9 MB/s | 78 kB 00:00 (131/285): libXft-devel-2.3.8-4.fc40.ppc64le.rp 892 kB/s | 36 kB 00:00 (132/285): libXi-1.8.1-3.fc40.ppc64le.rpm 1.1 MB/s | 43 kB 00:00 (133/285): libXi-devel-1.8.1-3.fc40.ppc64le.rpm 2.6 MB/s | 103 kB 00:00 (134/285): libXinerama-1.1.5-4.fc40.ppc64le.rpm 370 kB/s | 14 kB 00:00 (135/285): libXinerama-devel-1.1.5-4.fc40.ppc64 333 kB/s | 13 kB 00:00 (136/285): libXrandr-devel-1.5.4-1.fc40.ppc64le 616 kB/s | 19 kB 00:00 (137/285): libXrandr-1.5.4-1.fc40.ppc64le.rpm 851 kB/s | 28 kB 00:00 (138/285): libXrender-0.9.11-4.fc40.ppc64le.rpm 1.2 MB/s | 29 kB 00:00 (139/285): libXrender-devel-0.9.11-4.fc40.ppc64 792 kB/s | 19 kB 00:00 (140/285): libXt-1.3.0-1.fc40.ppc64le.rpm 5.3 MB/s | 197 kB 00:00 (141/285): libXt-devel-1.3.0-1.fc40.ppc64le.rpm 8.4 MB/s | 408 kB 00:00 (142/285): libXtst-1.2.4-4.fc40.ppc64le.rpm 883 kB/s | 22 kB 00:00 (143/285): libXv-1.0.12-1.fc40.ppc64le.rpm 887 kB/s | 19 kB 00:00 (144/285): libXv-devel-1.0.12-1.fc40.ppc64le.rp 1.9 MB/s | 38 kB 00:00 (145/285): libXxf86vm-1.1.5-4.fc40.ppc64le.rpm 969 kB/s | 18 kB 00:00 (146/285): libatomic-14.0.1-0.3.fc40.ppc64le.rp 466 kB/s | 22 kB 00:00 (147/285): libasan-14.0.1-0.3.fc40.ppc64le.rpm 5.6 MB/s | 498 kB 00:00 (148/285): libb2-0.98.1-9.fc39.ppc64le.rpm 409 kB/s | 25 kB 00:00 (149/285): libblkid-devel-2.39.3-4.fc40.ppc64le 323 kB/s | 18 kB 00:00 (150/285): libdrm-2.4.120-1.fc40.ppc64le.rpm 1.6 MB/s | 110 kB 00:00 (151/285): libedit-3.1-48.20230828cvs.fc40.ppc6 1.3 MB/s | 121 kB 00:00 (152/285): libevdev-1.13.1-2.fc39.ppc64le.rpm 1.2 MB/s | 44 kB 00:00 (153/285): libedit-devel-3.1-48.20230828cvs.fc4 385 kB/s | 40 kB 00:00 (154/285): libffi-devel-3.4.4-5.fc40.ppc64le.rp 726 kB/s | 28 kB 00:00 (155/285): java-17-openjdk-headless-17.0.10.0.7 27 MB/s | 44 MB 00:01 (156/285): libfontenc-1.1.7-1.fc40.ppc64le.rpm 115 kB/s | 33 kB 00:00 (157/285): libgfortran-14.0.1-0.3.fc40.ppc64le. 2.2 MB/s | 613 kB 00:00 (158/285): libglvnd-1.7.0-1.fc40.ppc64le.rpm 4.7 MB/s | 131 kB 00:00 (159/285): libglvnd-core-devel-1.7.0-1.fc40.ppc 591 kB/s | 17 kB 00:00 (160/285): libglvnd-devel-1.7.0-1.fc40.ppc64le. 3.7 MB/s | 157 kB 00:00 (161/285): libglvnd-egl-1.7.0-1.fc40.ppc64le.rp 2.0 MB/s | 41 kB 00:00 (162/285): libglvnd-gles-1.7.0-1.fc40.ppc64le.r 1.5 MB/s | 32 kB 00:00 (163/285): libglvnd-glx-1.7.0-1.fc40.ppc64le.rp 6.7 MB/s | 148 kB 00:00 (164/285): libglvnd-opengl-1.7.0-1.fc40.ppc64le 2.0 MB/s | 45 kB 00:00 (165/285): libgudev-238-2.fc39.ppc64le.rpm 1.5 MB/s | 34 kB 00:00 (166/285): libinput-1.25.0-1.fc40.ppc64le.rpm 6.9 MB/s | 220 kB 00:00 (167/285): libjpeg-turbo-2.1.4-5.fc40.ppc64le.r 8.3 MB/s | 208 kB 00:00 (168/285): libicu-devel-73.2-3.fc40.ppc64le.rpm 13 MB/s | 850 kB 00:00 (169/285): liblerc-4.0.0-4.fc39.ppc64le.rpm 7.8 MB/s | 220 kB 00:00 (170/285): libmng-2.0.3-19.fc39.ppc64le.rpm 8.0 MB/s | 206 kB 00:00 (171/285): libmount-devel-2.39.3-4.fc40.ppc64le 356 kB/s | 18 kB 00:00 (172/285): libmpc-1.3.1-3.fc39.ppc64le.rpm 1.9 MB/s | 95 kB 00:00 (173/285): libpng-1.6.40-1.fc40.ppc64le.rpm 2.3 MB/s | 137 kB 00:00 (174/285): libnauty-2.8.8-1.fc40.ppc64le.rpm 9.6 MB/s | 942 kB 00:00 (175/285): libpng-devel-1.6.40-1.fc40.ppc64le.r 6.7 MB/s | 294 kB 00:00 (176/285): libproxy-0.5.3-3.fc40.ppc64le.rpm 2.2 MB/s | 50 kB 00:00 (177/285): libquadmath-14.0.1-0.3.fc40.ppc64le. 8.7 MB/s | 199 kB 00:00 (178/285): libselinux-devel-3.6-2.fc40.ppc64le. 4.6 MB/s | 115 kB 00:00 (179/285): libsepol-devel-3.6-1.fc40.ppc64le.rp 1.8 MB/s | 40 kB 00:00 (180/285): libstdc++-static-14.0.1-0.3.fc40.ppc 18 MB/s | 1.0 MB 00:00 (181/285): libstdc++-devel-14.0.1-0.3.fc40.ppc6 34 MB/s | 2.6 MB 00:00 (182/285): libtiff-4.5.0-3.fc40.ppc64le.rpm 12 MB/s | 343 kB 00:00 (183/285): libtool-ltdl-2.4.7-10.fc40.ppc64le.r 1.6 MB/s | 40 kB 00:00 (184/285): libubsan-14.0.1-0.3.fc40.ppc64le.rpm 6.7 MB/s | 244 kB 00:00 (185/285): libuuid-devel-2.39.3-4.fc40.ppc64le. 806 kB/s | 25 kB 00:00 (186/285): libuv-1.47.0-3.fc40.ppc64le.rpm 5.3 MB/s | 260 kB 00:00 (187/285): libwacom-2.9.0-1.fc40.ppc64le.rpm 966 kB/s | 47 kB 00:00 (188/285): libicu-73.2-3.fc40.ppc64le.rpm 18 MB/s | 11 MB 00:00 (189/285): libwayland-client-1.22.0-2.fc39.ppc6 306 kB/s | 36 kB 00:00 (190/285): libwacom-data-2.9.0-1.fc40.noarch.rp 988 kB/s | 118 kB 00:00 (191/285): libwayland-server-1.22.0-2.fc39.ppc6 725 kB/s | 46 kB 00:00 (192/285): libwebp-1.3.2-4.fc40.ppc64le.rpm 4.1 MB/s | 269 kB 00:00 (193/285): libxcb-1.16-2.fc40.ppc64le.rpm 3.8 MB/s | 251 kB 00:00 (194/285): libxcrypt-devel-4.4.36-4.fc40.ppc64l 418 kB/s | 29 kB 00:00 (195/285): libxkbcommon-1.6.0-2.fc40.ppc64le.rp 2.1 MB/s | 154 kB 00:00 (196/285): libxkbcommon-x11-1.6.0-2.fc40.ppc64l 470 kB/s | 22 kB 00:00 (197/285): libxcb-devel-1.16-2.fc40.ppc64le.rpm 7.8 MB/s | 1.1 MB 00:00 (198/285): libxml2-devel-2.12.4-1.fc40.ppc64le. 7.4 MB/s | 495 kB 00:00 (199/285): libxshmfence-1.3.2-1.fc40.ppc64le.rp 252 kB/s | 12 kB 00:00 (200/285): lksctp-tools-1.0.19-4.fc39.ppc64le.r 1.0 MB/s | 96 kB 00:00 (201/285): llvm-googletest-17.0.6-2.fc40.ppc64l 8.2 MB/s | 368 kB 00:00 (202/285): llvm-devel-17.0.6-2.fc40.ppc64le.rpm 20 MB/s | 3.6 MB 00:00 (203/285): llvm-17.0.6-2.fc40.ppc64le.rpm 38 MB/s | 26 MB 00:00 (204/285): llvm-test-17.0.6-2.fc40.ppc64le.rpm 17 MB/s | 659 kB 00:00 (205/285): lua-5.4.6-3.fc39.ppc64le.rpm 4.9 MB/s | 201 kB 00:00 (206/285): lua-filesystem-1.8.0-9.fc39.ppc64le. 797 kB/s | 34 kB 00:00 (207/285): lua-json-1.3.4-4.fc39.noarch.rpm 1.1 MB/s | 26 kB 00:00 (208/285): lua-lpeg-1.0.2-11.fc39.ppc64le.rpm 2.2 MB/s | 70 kB 00:00 (209/285): lua-posix-36.2.1-3.fc39.ppc64le.rpm 5.4 MB/s | 143 kB 00:00 (210/285): lua-term-0.08-1.fc40.ppc64le.rpm 690 kB/s | 16 kB 00:00 (211/285): make-4.4.1-2.fc39.ppc64le.rpm 18 MB/s | 597 kB 00:00 (212/285): mesa-libEGL-24.0.0~rc2-4.fc40.ppc64l 5.7 MB/s | 150 kB 00:00 (213/285): mesa-libGL-24.0.0~rc2-4.fc40.ppc64le 7.5 MB/s | 197 kB 00:00 (214/285): mesa-libGLU-9.0.3-1.fc39.ppc64le.rpm 6.6 MB/s | 178 kB 00:00 (215/285): mesa-libGLU-devel-9.0.3-1.fc39.ppc64 476 kB/s | 12 kB 00:00 (216/285): mesa-libgbm-24.0.0~rc2-4.fc40.ppc64l 1.3 MB/s | 52 kB 00:00 (217/285): mesa-libglapi-24.0.0~rc2-4.fc40.ppc6 2.2 MB/s | 52 kB 00:00 (218/285): metis-5.1.0.3-3.fc40.ppc64le.rpm 17 MB/s | 598 kB 00:00 (219/285): mkfontscale-1.2.2-4.fc39.ppc64le.rpm 1.1 MB/s | 34 kB 00:00 (220/285): mockito-5.8.0-1.fc40.noarch.rpm 16 MB/s | 592 kB 00:00 (221/285): mpdecimal-2.5.1-7.fc39.ppc64le.rpm 3.2 MB/s | 104 kB 00:00 (222/285): mtdev-1.1.6-6.fc39.ppc64le.rpm 685 kB/s | 22 kB 00:00 (223/285): ncurses-c++-libs-6.4-9.20240113.fc40 1.4 MB/s | 39 kB 00:00 (224/285): ncurses-devel-6.4-9.20240113.fc40.pp 9.4 MB/s | 535 kB 00:00 (225/285): llvm-static-17.0.6-2.fc40.ppc64le.rp 28 MB/s | 36 MB 00:01 (226/285): llvm-libs-17.0.6-2.fc40.ppc64le.rpm 19 MB/s | 28 MB 00:01 (227/285): nettle-3.9.1-2.fc39.ppc64le.rpm 1.8 MB/s | 460 kB 00:00 (228/285): nspr-4.35.0-17.fc40.ppc64le.rpm 1.5 MB/s | 172 kB 00:00 (229/285): nss-softokn-3.96.1-1.fc40.ppc64le.rp 13 MB/s | 440 kB 00:00 (230/285): nss-3.96.1-1.fc40.ppc64le.rpm 17 MB/s | 790 kB 00:00 (231/285): nss-softokn-freebl-3.96.1-1.fc40.ppc 8.3 MB/s | 369 kB 00:00 (232/285): nss-sysinit-3.96.1-1.fc40.ppc64le.rp 659 kB/s | 19 kB 00:00 (233/285): nss-util-3.96.1-1.fc40.ppc64le.rpm 4.2 MB/s | 97 kB 00:00 (234/285): objenesis-3.3-4.fc40.noarch.rpm 4.2 MB/s | 115 kB 00:00 (235/285): objectweb-asm-9.6-1.fc40.noarch.rpm 11 MB/s | 362 kB 00:00 (236/285): openblas-0.3.26-1.fc40.ppc64le.rpm 1.6 MB/s | 38 kB 00:00 (237/285): opentest4j-1.3.0-2.fc40.noarch.rpm 1.1 MB/s | 26 kB 00:00 (238/285): pcre2-utf16-10.42-2.fc40.ppc64le.rpm 9.0 MB/s | 220 kB 00:00 (239/285): pcre2-utf32-10.42-2.fc40.ppc64le.rpm 5.9 MB/s | 207 kB 00:00 (240/285): pcre2-devel-10.42-2.fc40.ppc64le.rpm 5.1 MB/s | 473 kB 00:00 (241/285): pixman-0.43.0-1.fc40.ppc64le.rpm 8.4 MB/s | 230 kB 00:00 (242/285): procps-ng-4.0.4-1.fc40.ppc64le.rpm 12 MB/s | 391 kB 00:00 (243/285): pyproject-rpm-macros-1.12.0-1.fc40.n 1.8 MB/s | 41 kB 00:00 (244/285): python-rpm-macros-3.12-7.fc40.noarch 263 kB/s | 18 kB 00:00 (245/285): python3-3.12.1-2.fc40.ppc64le.rpm 510 kB/s | 27 kB 00:00 (246/285): python-pip-wheel-23.3.2-1.fc40.noarc 11 MB/s | 1.5 MB 00:00 (247/285): python3-devel-3.12.1-2.fc40.ppc64le. 9.5 MB/s | 274 kB 00:00 (248/285): openblas-openmp-0.3.26-1.fc40.ppc64l 15 MB/s | 4.6 MB 00:00 (249/285): python3-packaging-23.2-2.fc40.noarch 3.4 MB/s | 115 kB 00:00 (250/285): python3-rpm-generators-14-8.fc40.noa 1.2 MB/s | 30 kB 00:00 (251/285): python3-rpm-macros-3.12-7.fc40.noarc 627 kB/s | 13 kB 00:00 (252/285): python3-setuptools-68.2.2-1.fc40.noa 24 MB/s | 1.4 MB 00:00 (253/285): qt-common-4.8.7-74.fc39.noarch.rpm 324 kB/s | 7.7 kB 00:00 (254/285): qt-4.8.7-74.fc39.ppc64le.rpm 20 MB/s | 4.7 MB 00:00 (255/285): qt-settings-39.1-3.fc40.noarch.rpm 464 kB/s | 9.8 kB 00:00 (256/285): python3-libs-3.12.1-2.fc40.ppc64le.r 23 MB/s | 9.0 MB 00:00 (257/285): qt-devel-4.8.7-74.fc39.ppc64le.rpm 23 MB/s | 9.8 MB 00:00 (258/285): qt5-qtbase-5.15.12-1.fc40.ppc64le.rp 20 MB/s | 3.8 MB 00:00 (259/285): qt5-qtbase-common-5.15.12-1.fc40.noa 482 kB/s | 12 kB 00:00 (260/285): rhash-1.4.3-3.fc39.ppc64le.rpm 7.6 MB/s | 206 kB 00:00 (261/285): scotch-7.0.4-2.fc40.ppc64le.rpm 11 MB/s | 341 kB 00:00 (262/285): scotch-devel-7.0.4-2.fc40.ppc64le.rp 329 kB/s | 25 kB 00:00 (263/285): sysprof-capture-devel-45.1-1.fc40.pp 1.0 MB/s | 62 kB 00:00 (264/285): tcl-8.6.13-1.fc40.ppc64le.rpm 7.6 MB/s | 1.2 MB 00:00 (265/285): ttmkfdir-3.0.9-69.fc39.ppc64le.rpm 1.3 MB/s | 56 kB 00:00 (266/285): tzdata-2023d-2.fc40.noarch.rpm 9.0 MB/s | 434 kB 00:00 (267/285): qt5-qtbase-gui-5.15.12-1.fc40.ppc64l 14 MB/s | 7.0 MB 00:00 (268/285): tzdata-java-2023d-2.fc40.noarch.rpm 968 kB/s | 47 kB 00:00 (269/285): vim-filesystem-9.1.031-1.fc40.noarch 842 kB/s | 17 kB 00:00 (270/285): xcb-util-0.4.1-3.fc39.ppc64le.rpm 638 kB/s | 19 kB 00:00 (271/285): unixODBC-2.3.12-2.fc40.ppc64le.rpm 7.4 MB/s | 498 kB 00:00 (272/285): xcb-util-image-0.4.1-3.fc39.ppc64le. 214 kB/s | 20 kB 00:00 (273/285): xcb-util-keysyms-0.4.1-3.fc39.ppc64l 189 kB/s | 15 kB 00:00 (274/285): qt-x11-4.8.7-74.fc39.ppc64le.rpm 13 MB/s | 13 MB 00:00 (275/285): xcb-util-renderutil-0.3.10-3.fc39.pp 180 kB/s | 18 kB 00:00 (276/285): xcb-util-wm-0.4.2-3.fc39.ppc64le.rpm 322 kB/s | 32 kB 00:00 (277/285): xml-common-0.6.3-62.fc40.noarch.rpm 408 kB/s | 31 kB 00:00 (278/285): xorg-x11-proto-devel-2023.2-3.fc40.n 6.3 MB/s | 263 kB 00:00 (279/285): xorg-x11-fonts-Type1-7.5-37.fc40.noa 4.0 MB/s | 499 kB 00:00 (280/285): xkeyboard-config-2.40-2.fc40.noarch. 5.7 MB/s | 917 kB 00:00 (281/285): xz-devel-5.4.5-1.fc40.ppc64le.rpm 1.0 MB/s | 62 kB 00:00 (282/285): zlib-ng-compat-devel-2.1.6-1.fc40.pp 624 kB/s | 36 kB 00:00 (283/285): java-1.8.0-openjdk-1.8.0.392.b08-7.f 1.6 MB/s | 487 kB 00:00 (284/285): java-1.8.0-openjdk-devel-1.8.0.392.b 12 MB/s | 7.4 MB 00:00 (285/285): java-1.8.0-openjdk-headless-1.8.0.39 26 MB/s | 33 MB 00:01 -------------------------------------------------------------------------------- Total 41 MB/s | 411 MB 00:09 updates 1.6 MB/s | 1.6 kB 00:00 Key imported successfully Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: copy-jdk-configs-4.1-3.fc39.noarch 1/1 Running scriptlet: java-17-openjdk-headless-1:17.0.10.0.7-1.fc40.ppc64l 1/1 Running scriptlet: java-1.8.0-openjdk-headless-1:1.8.0.392.b08-7.fc39.p 1/1 Preparing : 1/1 Installing : xorg-x11-proto-devel-2023.2-3.fc40.noarch 1/285 Installing : javapackages-filesystem-6.2.0-5.fc40.noarch 2/285 Installing : boost-system-1.83.0-2.fc40.ppc64le 3/285 Installing : libicu-73.2-3.fc40.ppc64le 4/285 Installing : boost-chrono-1.83.0-2.fc40.ppc64le 5/285 Installing : cmake-filesystem-3.27.7-1.fc40.ppc64le 6/285 Installing : boost-thread-1.83.0-2.fc40.ppc64le 7/285 Installing : nspr-4.35.0-17.fc40.ppc64le 8/285 Installing : libpng-2:1.6.40-1.fc40.ppc64le 9/285 Installing : libglvnd-1:1.7.0-1.fc40.ppc64le 10/285 Installing : libICE-1.1.1-1.fc40.ppc64le 11/285 Installing : expat-2.5.0-3.fc39.ppc64le 12/285 Installing : libSM-1.2.4-1.fc40.ppc64le 13/285 Installing : nss-util-3.96.1-1.fc40.ppc64le 14/285 Installing : zlib-ng-compat-devel-2.1.6-1.fc40.ppc64le 15/285 Installing : libjpeg-turbo-2.1.4-5.fc40.ppc64le 16/285 Installing : libdrm-2.4.120-1.fc40.ppc64le 17/285 Installing : libX11-xcb-1.8.7-1.fc40.ppc64le 18/285 Installing : libICE-devel-1.1.1-1.fc40.ppc64le 19/285 Installing : boost-regex-1.83.0-2.fc40.ppc64le 20/285 Installing : python-rpm-macros-3.12-7.fc40.noarch 21/285 Installing : libmpc-1.3.1-3.fc39.ppc64le 22/285 Installing : libgfortran-14.0.1-0.3.fc40.ppc64le 23/285 Installing : fonts-filesystem-1:2.0.5-12.fc39.noarch 24/285 Installing : dbus-libs-1:1.14.10-1.fc40.ppc64le 25/285 Installing : alsa-lib-1.2.10-3.fc40.ppc64le 26/285 Installing : boost-context-1.83.0-2.fc40.ppc64le 27/285 Installing : boost-atomic-1.83.0-2.fc40.ppc64le 28/285 Installing : boost-filesystem-1.83.0-2.fc40.ppc64le 29/285 Installing : python3-rpm-macros-3.12-7.fc40.noarch 30/285 Installing : libglvnd-opengl-1:1.7.0-1.fc40.ppc64le 31/285 Installing : libicu-devel-73.2-3.fc40.ppc64le 32/285 Installing : tzdata-java-2023d-2.fc40.noarch 33/285 Installing : scotch-7.0.4-2.fc40.ppc64le 34/285 Installing : qt-settings-39.1-3.fc40.noarch 35/285 Installing : pcre2-utf16-10.42-2.fc40.ppc64le 36/285 Installing : mesa-libglapi-24.0.0~rc2-4.fc40.ppc64le 37/285 Installing : lua-posix-36.2.1-3.fc39.ppc64le 38/285 Installing : lua-5.4.6-3.fc39.ppc64le 39/285 Installing : copy-jdk-configs-4.1-3.fc39.noarch 40/285 Installing : lksctp-tools-1.0.19-4.fc39.ppc64le 41/285 Installing : libxshmfence-1.3.2-1.fc40.ppc64le 42/285 Installing : libwayland-server-1.22.0-2.fc39.ppc64le 43/285 Installing : libtool-ltdl-2.4.7-10.fc40.ppc64le 44/285 Installing : libstdc++-devel-14.0.1-0.3.fc40.ppc64le 45/285 Installing : libevdev-1.13.1-2.fc39.ppc64le 46/285 Installing : libedit-3.1-48.20230828cvs.fc40.ppc64le 47/285 Installing : llvm-libs-17.0.6-2.fc40.ppc64le 48/285 Installing : libXau-1.0.11-4.fc40.ppc64le 49/285 Installing : libxcb-1.16-2.fc40.ppc64le 50/285 Installing : mesa-libgbm-24.0.0~rc2-4.fc40.ppc64le 51/285 Installing : gettext-libs-0.22-2.fc39.ppc64le 52/285 Installing : graphite2-1.3.14-13.fc40.ppc64le 53/285 Installing : boost-date-time-1.83.0-2.fc40.ppc64le 54/285 Installing : boost-container-1.83.0-2.fc40.ppc64le 55/285 Installing : boost-json-1.83.0-2.fc40.ppc64le 56/285 Installing : boost-wave-1.83.0-2.fc40.ppc64le 57/285 Installing : graphite2-devel-1.3.14-13.fc40.ppc64le 58/285 Installing : xcb-util-0.4.1-3.fc39.ppc64le 59/285 Installing : xcb-util-image-0.4.1-3.fc39.ppc64le 60/285 Installing : xcb-util-keysyms-0.4.1-3.fc39.ppc64le 61/285 Installing : xcb-util-renderutil-0.3.10-3.fc39.ppc64le 62/285 Installing : xcb-util-wm-0.4.2-3.fc39.ppc64le 63/285 Installing : libXau-devel-1.0.11-4.fc40.ppc64le 64/285 Installing : libxcb-devel-1.16-2.fc40.ppc64le 65/285 Installing : unixODBC-2.3.12-2.fc40.ppc64le 66/285 Installing : lua-term-0.08-1.fc40.ppc64le 67/285 Installing : scotch-devel-7.0.4-2.fc40.ppc64le 68/285 Installing : mesa-libGLU-9.0.3-1.fc39.ppc64le 69/285 Installing : pyproject-rpm-macros-1.12.0-1.fc40.noarch 70/285 Installing : boost-fiber-1.83.0-2.fc40.ppc64le 71/285 Installing : boost-log-1.83.0-2.fc40.ppc64le 72/285 Installing : boost-coroutine-1.83.0-2.fc40.ppc64le 73/285 Installing : avahi-libs-0.8-24.fc39.ppc64le 74/285 Installing : abattis-cantarell-vf-fonts-0.301-10.fc39.noarch 75/285 Installing : cpp-14.0.1-0.3.fc40.ppc64le 76/285 Installing : boost-graph-1.83.0-2.fc40.ppc64le 77/285 Installing : libpng-devel-2:1.6.40-1.fc40.ppc64le 78/285 Installing : nss-softokn-freebl-3.96.1-1.fc40.ppc64le 79/285 Installing : nss-softokn-3.96.1-1.fc40.ppc64le 80/285 Installing : boost-locale-1.83.0-2.fc40.ppc64le 81/285 Installing : boost-type_erasure-1.83.0-2.fc40.ppc64le 82/285 Installing : boost-timer-1.83.0-2.fc40.ppc64le 83/285 Installing : xz-devel-5.4.5-1.fc40.ppc64le 84/285 Installing : libxml2-devel-2.12.4-1.fc40.ppc64le 85/285 Running scriptlet: xml-common-0.6.3-62.fc40.noarch 86/285 Installing : xml-common-0.6.3-62.fc40.noarch 86/285 Installing : xkeyboard-config-2.40-2.fc40.noarch 87/285 Installing : libxkbcommon-1.6.0-2.fc40.ppc64le 88/285 Installing : libxkbcommon-x11-1.6.0-2.fc40.ppc64le 89/285 Installing : vim-filesystem-2:9.1.031-1.fc40.noarch 90/285 Installing : tzdata-2023d-2.fc40.noarch 91/285 Installing : tcl-1:8.6.13-1.fc40.ppc64le 92/285 Installing : sysprof-capture-devel-45.1-1.fc40.ppc64le 93/285 Installing : rhash-1.4.3-3.fc39.ppc64le 94/285 Installing : python-pip-wheel-23.3.2-1.fc40.noarch 95/285 Installing : procps-ng-4.0.4-1.fc40.ppc64le 96/285 Installing : pixman-0.43.0-1.fc40.ppc64le 97/285 Installing : pcre2-utf32-10.42-2.fc40.ppc64le 98/285 Installing : pcre2-devel-10.42-2.fc40.ppc64le 99/285 Installing : openblas-0.3.26-1.fc40.ppc64le 100/285 Installing : openblas-openmp-0.3.26-1.fc40.ppc64le 101/285 Installing : nettle-3.9.1-2.fc39.ppc64le 102/285 Installing : gnutls-3.8.3-2.fc40.ppc64le 103/285 Installing : glib2-2.79.1-1.fc40.ppc64le 104/285 Installing : qt-common-1:4.8.7-74.fc39.noarch 105/285 Running scriptlet: qt-1:4.8.7-74.fc39.ppc64le 106/285 Installing : qt-1:4.8.7-74.fc39.ppc64le 106/285 Running scriptlet: qt-1:4.8.7-74.fc39.ppc64le 106/285 Installing : cups-libs-1:2.4.7-7.fc40.ppc64le 107/285 Installing : libgudev-238-2.fc39.ppc64le 108/285 Installing : ncurses-c++-libs-6.4-9.20240113.fc40.ppc64le 109/285 Installing : ncurses-devel-6.4-9.20240113.fc40.ppc64le 110/285 Installing : libedit-devel-3.1-48.20230828cvs.fc40.ppc64le 111/285 Installing : mtdev-1.1.6-6.fc39.ppc64le 112/285 Installing : mpdecimal-2.5.1-7.fc39.ppc64le 113/285 Installing : metis-5.1.0.3-3.fc40.ppc64le 114/285 Installing : lua-lpeg-1.0.2-11.fc39.ppc64le 115/285 Installing : lua-json-1.3.4-4.fc39.noarch 116/285 Installing : lua-filesystem-1.8.0-9.fc39.ppc64le 117/285 Installing : Lmod-8.7.32-1.fc40.ppc64le 118/285 Running scriptlet: Lmod-8.7.32-1.fc40.ppc64le 118/285 Installing : llvm-static-17.0.6-2.fc40.ppc64le 119/285 Installing : llvm-googletest-17.0.6-2.fc40.ppc64le 120/285 Installing : libwebp-1.3.2-4.fc40.ppc64le 121/285 Installing : libwayland-client-1.22.0-2.fc39.ppc64le 122/285 Installing : libglvnd-egl-1:1.7.0-1.fc40.ppc64le 123/285 Installing : mesa-libEGL-24.0.0~rc2-4.fc40.ppc64le 124/285 Installing : libglvnd-gles-1:1.7.0-1.fc40.ppc64le 125/285 Installing : libwacom-data-2.9.0-1.fc40.noarch 126/285 Installing : libuv-1:1.47.0-3.fc40.ppc64le 127/285 Installing : libuuid-devel-2.39.3-4.fc40.ppc64le 128/285 Installing : libSM-devel-1.2.4-1.fc40.ppc64le 129/285 Installing : libubsan-14.0.1-0.3.fc40.ppc64le 130/285 Installing : libsepol-devel-3.6-1.fc40.ppc64le 131/285 Installing : libselinux-devel-3.6-2.fc40.ppc64le 132/285 Installing : libquadmath-14.0.1-0.3.fc40.ppc64le 133/285 Installing : flexiblas-netlib-3.4.1-3.fc40.ppc64le 134/285 Installing : flexiblas-openblas-openmp-3.4.1-3.fc40.ppc64le 135/285 Installing : flexiblas-3.4.1-3.fc40.ppc64le 136/285 Installing : suitesparse-5.13.0-4.fc40.ppc64le 137/285 Installing : glpk-5.0-10.fc40.ppc64le 138/285 Installing : coin-or-CoinUtils-2.11.4-12.fc40.ppc64le 139/285 Installing : coin-or-Osi-0.108.6-11.fc40.ppc64le 140/285 Installing : liblerc-4.0.0-4.fc39.ppc64le 141/285 Installing : libglvnd-core-devel-1:1.7.0-1.fc40.ppc64le 142/285 Installing : libfontenc-1.1.7-1.fc40.ppc64le 143/285 Installing : libffi-devel-3.4.4-5.fc40.ppc64le 144/285 Installing : libblkid-devel-2.39.3-4.fc40.ppc64le 145/285 Installing : libmount-devel-2.39.3-4.fc40.ppc64le 146/285 Installing : libb2-0.98.1-9.fc39.ppc64le 147/285 Installing : python3-3.12.1-2.fc40.ppc64le 148/285 Installing : python3-libs-3.12.1-2.fc40.ppc64le 149/285 Installing : boost-python3-1.83.0-2.fc40.ppc64le 150/285 Installing : cmake-rpm-macros-3.27.7-1.fc40.noarch 151/285 Installing : llvm-17.0.6-2.fc40.ppc64le 152/285 Installing : python3-packaging-23.2-2.fc40.noarch 153/285 Installing : glib2-devel-2.79.1-1.fc40.ppc64le 154/285 Installing : python3-rpm-generators-14-8.fc40.noarch 155/285 Installing : llvm-test-17.0.6-2.fc40.ppc64le 156/285 Installing : python3-numpy-1:1.26.2-4.fc40.ppc64le 157/285 Installing : boost-numpy3-1.83.0-2.fc40.ppc64le 158/285 Installing : crypto-policies-scripts-20231204-1.git1e3a2e4.fc 159/285 Installing : nss-sysinit-3.96.1-1.fc40.ppc64le 160/285 Installing : nss-3.96.1-1.fc40.ppc64le 161/285 Running scriptlet: nss-3.96.1-1.fc40.ppc64le 161/285 Installing : java-17-openjdk-headless-1:17.0.10.0.7-1.fc40.pp 162/285 Running scriptlet: java-17-openjdk-headless-1:17.0.10.0.7-1.fc40.pp 162/285 Installing : javapackages-tools-6.2.0-5.fc40.noarch 163/285 Installing : libwacom-2.9.0-1.fc40.ppc64le 164/285 Installing : libinput-1.25.0-1.fc40.ppc64le 165/285 Running scriptlet: libinput-1.25.0-1.fc40.ppc64le 165/285 Installing : libatomic-14.0.1-0.3.fc40.ppc64le 166/285 Installing : libasan-14.0.1-0.3.fc40.ppc64le 167/285 Installing : libX11-common-1.8.7-1.fc40.noarch 168/285 Installing : libX11-1.8.7-1.fc40.ppc64le 169/285 Installing : libXext-1.3.5-5.fc40.ppc64le 170/285 Installing : libX11-devel-1.8.7-1.fc40.ppc64le 171/285 Installing : libXrender-0.9.11-4.fc40.ppc64le 172/285 Installing : libXext-devel-1.3.5-5.fc40.ppc64le 173/285 Installing : libXrender-devel-0.9.11-4.fc40.ppc64le 174/285 Installing : libXi-1.8.1-3.fc40.ppc64le 175/285 Installing : libXfixes-6.0.1-1.fc40.ppc64le 176/285 Installing : libXfixes-devel-6.0.1-1.fc40.ppc64le 177/285 Installing : libXcursor-1.2.1-5.fc40.ppc64le 178/285 Installing : libXrandr-1.5.4-1.fc40.ppc64le 179/285 Installing : libXinerama-1.1.5-4.fc40.ppc64le 180/285 Installing : libXinerama-devel-1.1.5-4.fc40.ppc64le 181/285 Installing : libXrandr-devel-1.5.4-1.fc40.ppc64le 182/285 Installing : libXcursor-devel-1.2.1-5.fc40.ppc64le 183/285 Installing : libXi-devel-1.8.1-3.fc40.ppc64le 184/285 Installing : libXtst-1.2.4-4.fc40.ppc64le 185/285 Installing : libXv-1.0.12-1.fc40.ppc64le 186/285 Installing : libXv-devel-1.0.12-1.fc40.ppc64le 187/285 Installing : libXxf86vm-1.1.5-4.fc40.ppc64le 188/285 Installing : libglvnd-glx-1:1.7.0-1.fc40.ppc64le 189/285 Installing : mesa-libGL-24.0.0~rc2-4.fc40.ppc64le 190/285 Installing : libglvnd-devel-1:1.7.0-1.fc40.ppc64le 191/285 Installing : glx-utils-9.0.0-4.fc40.ppc64le 192/285 Installing : libXcomposite-0.4.6-1.fc40.ppc64le 193/285 Installing : libXt-1.3.0-1.fc40.ppc64le 194/285 Installing : libXt-devel-1.3.0-1.fc40.ppc64le 195/285 Installing : lcms2-2.16-2.fc40.ppc64le 196/285 Installing : libmng-2.0.3-19.fc39.ppc64le 197/285 Installing : kernel-headers-6.8.0-0.rc1.12.fc40.ppc64le 198/285 Installing : libxcrypt-devel-4.4.36-4.fc40.ppc64le 199/285 Installing : glibc-devel-2.38.9000-35.fc40.ppc64le 200/285 Installing : jsoncpp-1.9.5-5.fc39.ppc64le 201/285 Installing : jbigkit-libs-2.1-27.fc40.ppc64le 202/285 Installing : libtiff-4.5.0-3.fc40.ppc64le 203/285 Installing : gsl-2.7.1-5.fc39.ppc64le 204/285 Installing : google-noto-fonts-common-20230801-4.fc40.noarch 205/285 Installing : google-noto-sans-vf-fonts-20230801-4.fc40.noarch 206/285 Installing : default-fonts-core-sans-4.0-9.fc40.noarch 207/285 Installing : cairo-1.18.0-1.fc40.ppc64le 208/285 Installing : harfbuzz-8.3.0-2.fc40.ppc64le 209/285 Installing : freetype-2.13.2-1.fc40.ppc64le 210/285 Installing : fontconfig-2.15.0-1.fc40.ppc64le 211/285 Running scriptlet: fontconfig-2.15.0-1.fc40.ppc64le 211/285 Installing : java-1.8.0-openjdk-headless-1:1.8.0.392.b08-7.fc 212/285 Running scriptlet: java-1.8.0-openjdk-headless-1:1.8.0.392.b08-7.fc 212/285 Installing : byte-buddy-agent-1.14.2-4.fc40.noarch 213/285 Installing : hamcrest-2.2-12.fc40.noarch 214/285 Installing : junit-1:4.13.2-2.fc40.noarch 215/285 Installing : objectweb-asm-9.6-1.fc40.noarch 216/285 Installing : byte-buddy-1.14.2-4.fc40.noarch 217/285 Installing : objenesis-3.3-4.fc40.noarch 218/285 Installing : opentest4j-1.3.0-2.fc40.noarch 219/285 Installing : mockito-5.8.0-1.fc40.noarch 220/285 Installing : jacop-4.9.0-2.fc39.noarch 221/285 Installing : libXft-2.3.8-4.fc40.ppc64le 222/285 Installing : qt-x11-1:4.8.7-74.fc39.ppc64le 223/285 Installing : mkfontscale-1.2.2-4.fc39.ppc64le 224/285 Installing : ttmkfdir-3.0.9-69.fc39.ppc64le 225/285 Installing : xorg-x11-fonts-Type1-7.5-37.fc40.noarch 226/285 Running scriptlet: xorg-x11-fonts-Type1-7.5-37.fc40.noarch 226/285 Installing : java-1.8.0-openjdk-1:1.8.0.392.b08-7.fc39.ppc64l 227/285 Running scriptlet: java-1.8.0-openjdk-1:1.8.0.392.b08-7.fc39.ppc64l 227/285 Installing : harfbuzz-icu-8.3.0-2.fc40.ppc64le 228/285 Installing : gl-manpages-1.1-29.20190306.fc40.noarch 229/285 Installing : mesa-libGLU-devel-9.0.3-1.fc39.ppc64le 230/285 Installing : gettext-envsubst-0.22-2.fc39.ppc64le 231/285 Installing : gettext-runtime-0.22-2.fc39.ppc64le 232/285 Installing : gettext-0.22-2.fc39.ppc64le 233/285 Installing : gc-8.2.2-4.fc39.ppc64le 234/285 Installing : guile22-2.2.7-9.fc39.ppc64le 235/285 Installing : make-1:4.4.1-2.fc39.ppc64le 236/285 Installing : gcc-14.0.1-0.3.fc40.ppc64le 237/285 Running scriptlet: gcc-14.0.1-0.3.fc40.ppc64le 237/285 Installing : gcc-c++-14.0.1-0.3.fc40.ppc64le 238/285 Installing : emacs-filesystem-1:29.2-2.fc40.noarch 239/285 Installing : cmake-data-3.27.7-1.fc40.noarch 240/285 Installing : cmake-3.27.7-1.fc40.ppc64le 241/285 Installing : duktape-2.7.0-5.fc39.ppc64le 242/285 Installing : libproxy-0.5.3-3.fc40.ppc64le 243/285 Installing : double-conversion-3.3.0-1.fc40.ppc64le 244/285 Installing : qt5-qtbase-common-5.15.12-1.fc40.noarch 245/285 Running scriptlet: qt5-qtbase-5.15.12-1.fc40.ppc64le 246/285 Installing : qt5-qtbase-5.15.12-1.fc40.ppc64le 246/285 Running scriptlet: qt5-qtbase-5.15.12-1.fc40.ppc64le 246/285 Installing : qt5-qtbase-gui-5.15.12-1.fc40.ppc64le 247/285 Installing : gecode-6.2.0-13.fc39.ppc64le 248/285 Installing : mp-3.1.0-42.20200303git7fd4828.fc39.ppc64le 249/285 Installing : cliquer-libs-1.22-6.fc39.ppc64le 250/285 Installing : libnauty-2.8.8-1.fc40.ppc64le 251/285 Installing : bzip2-devel-1.0.8-16.fc39.ppc64le 252/285 Installing : brotli-1.1.0-1.fc40.ppc64le 253/285 Installing : brotli-devel-1.1.0-1.fc40.ppc64le 254/285 Installing : freetype-devel-2.13.2-1.fc40.ppc64le 255/285 Installing : harfbuzz-devel-8.3.0-2.fc40.ppc64le 256/285 Installing : fontconfig-devel-2.15.0-1.fc40.ppc64le 257/285 Installing : libXft-devel-2.3.8-4.fc40.ppc64le 258/285 Installing : annobin-docs-12.38-1.fc40.noarch 259/285 Installing : boost-test-1.83.0-2.fc40.ppc64le 260/285 Installing : boost-stacktrace-1.83.0-2.fc40.ppc64le 261/285 Installing : boost-serialization-1.83.0-2.fc40.ppc64le 262/285 Installing : boost-random-1.83.0-2.fc40.ppc64le 263/285 Installing : boost-program-options-1.83.0-2.fc40.ppc64le 264/285 Installing : boost-nowide-1.83.0-2.fc40.ppc64le 265/285 Installing : boost-math-1.83.0-2.fc40.ppc64le 266/285 Installing : boost-iostreams-1.83.0-2.fc40.ppc64le 267/285 Installing : boost-contract-1.83.0-2.fc40.ppc64le 268/285 Installing : boost-1.83.0-2.fc40.ppc64le 269/285 Installing : MUMPS-common-5.6.2-3.fc40.noarch 270/285 Installing : MUMPS-5.6.2-3.fc40.ppc64le 271/285 Installing : coin-or-Cbc-2.10.5-16.fc40.ppc64le 272/285 Installing : coin-or-Clp-1.17.6-17.fc40.ppc64le 273/285 Installing : coin-or-Cgl-0.60.3-12.fc40.ppc64le 274/285 Installing : coin-or-lemon-1.3.1-29.fc40.ppc64le 275/285 Installing : coin-or-lemon-devel-1.3.1-29.fc40.ppc64le 276/285 Installing : boost-devel-1.83.0-2.fc40.ppc64le 277/285 Installing : annobin-plugin-gcc-12.38-1.fc40.ppc64le 278/285 Running scriptlet: annobin-plugin-gcc-12.38-1.fc40.ppc64le 278/285 Installing : qt-devel-1:4.8.7-74.fc39.ppc64le 279/285 Installing : gcc-plugin-annobin-14.0.1-0.3.fc40.ppc64le 280/285 Running scriptlet: gcc-plugin-annobin-14.0.1-0.3.fc40.ppc64le 280/285 Installing : java-1.8.0-openjdk-devel-1:1.8.0.392.b08-7.fc39. 281/285 Running scriptlet: java-1.8.0-openjdk-devel-1:1.8.0.392.b08-7.fc39. 281/285 Installing : llvm-devel-17.0.6-2.fc40.ppc64le 282/285 Running scriptlet: llvm-devel-17.0.6-2.fc40.ppc64le 282/285 Installing : python3-devel-3.12.1-2.fc40.ppc64le 283/285 Installing : python3-setuptools-68.2.2-1.fc40.noarch 284/285 Installing : libstdc++-static-14.0.1-0.3.fc40.ppc64le 285/285 Running scriptlet: copy-jdk-configs-4.1-3.fc39.noarch 285/285 Running scriptlet: crypto-policies-scripts-20231204-1.git1e3a2e4.fc 285/285 Running scriptlet: nss-3.96.1-1.fc40.ppc64le 285/285 Running scriptlet: java-17-openjdk-headless-1:17.0.10.0.7-1.fc40.pp 285/285 Running scriptlet: fontconfig-2.15.0-1.fc40.ppc64le 285/285 Running scriptlet: java-1.8.0-openjdk-headless-1:1.8.0.392.b08-7.fc 285/285 Running scriptlet: java-1.8.0-openjdk-1:1.8.0.392.b08-7.fc39.ppc64l 285/285 Running scriptlet: java-1.8.0-openjdk-devel-1:1.8.0.392.b08-7.fc39. 285/285 Running scriptlet: libstdc++-static-14.0.1-0.3.fc40.ppc64le 285/285 Installed: Lmod-8.7.32-1.fc40.ppc64le MUMPS-5.6.2-3.fc40.ppc64le MUMPS-common-5.6.2-3.fc40.noarch abattis-cantarell-vf-fonts-0.301-10.fc39.noarch alsa-lib-1.2.10-3.fc40.ppc64le annobin-docs-12.38-1.fc40.noarch annobin-plugin-gcc-12.38-1.fc40.ppc64le avahi-libs-0.8-24.fc39.ppc64le boost-1.83.0-2.fc40.ppc64le boost-atomic-1.83.0-2.fc40.ppc64le boost-chrono-1.83.0-2.fc40.ppc64le boost-container-1.83.0-2.fc40.ppc64le boost-context-1.83.0-2.fc40.ppc64le boost-contract-1.83.0-2.fc40.ppc64le boost-coroutine-1.83.0-2.fc40.ppc64le boost-date-time-1.83.0-2.fc40.ppc64le boost-devel-1.83.0-2.fc40.ppc64le boost-fiber-1.83.0-2.fc40.ppc64le boost-filesystem-1.83.0-2.fc40.ppc64le boost-graph-1.83.0-2.fc40.ppc64le boost-iostreams-1.83.0-2.fc40.ppc64le boost-json-1.83.0-2.fc40.ppc64le boost-locale-1.83.0-2.fc40.ppc64le boost-log-1.83.0-2.fc40.ppc64le boost-math-1.83.0-2.fc40.ppc64le boost-nowide-1.83.0-2.fc40.ppc64le boost-numpy3-1.83.0-2.fc40.ppc64le boost-program-options-1.83.0-2.fc40.ppc64le boost-python3-1.83.0-2.fc40.ppc64le boost-random-1.83.0-2.fc40.ppc64le boost-regex-1.83.0-2.fc40.ppc64le boost-serialization-1.83.0-2.fc40.ppc64le boost-stacktrace-1.83.0-2.fc40.ppc64le boost-system-1.83.0-2.fc40.ppc64le boost-test-1.83.0-2.fc40.ppc64le boost-thread-1.83.0-2.fc40.ppc64le boost-timer-1.83.0-2.fc40.ppc64le boost-type_erasure-1.83.0-2.fc40.ppc64le boost-wave-1.83.0-2.fc40.ppc64le brotli-1.1.0-1.fc40.ppc64le brotli-devel-1.1.0-1.fc40.ppc64le byte-buddy-1.14.2-4.fc40.noarch byte-buddy-agent-1.14.2-4.fc40.noarch bzip2-devel-1.0.8-16.fc39.ppc64le cairo-1.18.0-1.fc40.ppc64le cliquer-libs-1.22-6.fc39.ppc64le cmake-3.27.7-1.fc40.ppc64le cmake-data-3.27.7-1.fc40.noarch cmake-filesystem-3.27.7-1.fc40.ppc64le cmake-rpm-macros-3.27.7-1.fc40.noarch coin-or-Cbc-2.10.5-16.fc40.ppc64le coin-or-Cgl-0.60.3-12.fc40.ppc64le coin-or-Clp-1.17.6-17.fc40.ppc64le coin-or-CoinUtils-2.11.4-12.fc40.ppc64le coin-or-Osi-0.108.6-11.fc40.ppc64le coin-or-lemon-1.3.1-29.fc40.ppc64le coin-or-lemon-devel-1.3.1-29.fc40.ppc64le copy-jdk-configs-4.1-3.fc39.noarch cpp-14.0.1-0.3.fc40.ppc64le crypto-policies-scripts-20231204-1.git1e3a2e4.fc40.noarch cups-libs-1:2.4.7-7.fc40.ppc64le dbus-libs-1:1.14.10-1.fc40.ppc64le default-fonts-core-sans-4.0-9.fc40.noarch double-conversion-3.3.0-1.fc40.ppc64le duktape-2.7.0-5.fc39.ppc64le emacs-filesystem-1:29.2-2.fc40.noarch expat-2.5.0-3.fc39.ppc64le flexiblas-3.4.1-3.fc40.ppc64le flexiblas-netlib-3.4.1-3.fc40.ppc64le flexiblas-openblas-openmp-3.4.1-3.fc40.ppc64le fontconfig-2.15.0-1.fc40.ppc64le fontconfig-devel-2.15.0-1.fc40.ppc64le fonts-filesystem-1:2.0.5-12.fc39.noarch freetype-2.13.2-1.fc40.ppc64le freetype-devel-2.13.2-1.fc40.ppc64le gc-8.2.2-4.fc39.ppc64le gcc-14.0.1-0.3.fc40.ppc64le gcc-c++-14.0.1-0.3.fc40.ppc64le gcc-plugin-annobin-14.0.1-0.3.fc40.ppc64le gecode-6.2.0-13.fc39.ppc64le gettext-0.22-2.fc39.ppc64le gettext-envsubst-0.22-2.fc39.ppc64le gettext-libs-0.22-2.fc39.ppc64le gettext-runtime-0.22-2.fc39.ppc64le gl-manpages-1.1-29.20190306.fc40.noarch glib2-2.79.1-1.fc40.ppc64le glib2-devel-2.79.1-1.fc40.ppc64le glibc-devel-2.38.9000-35.fc40.ppc64le glpk-5.0-10.fc40.ppc64le glx-utils-9.0.0-4.fc40.ppc64le gnutls-3.8.3-2.fc40.ppc64le google-noto-fonts-common-20230801-4.fc40.noarch google-noto-sans-vf-fonts-20230801-4.fc40.noarch graphite2-1.3.14-13.fc40.ppc64le graphite2-devel-1.3.14-13.fc40.ppc64le gsl-2.7.1-5.fc39.ppc64le guile22-2.2.7-9.fc39.ppc64le hamcrest-2.2-12.fc40.noarch harfbuzz-8.3.0-2.fc40.ppc64le harfbuzz-devel-8.3.0-2.fc40.ppc64le harfbuzz-icu-8.3.0-2.fc40.ppc64le jacop-4.9.0-2.fc39.noarch java-1.8.0-openjdk-1:1.8.0.392.b08-7.fc39.ppc64le java-1.8.0-openjdk-devel-1:1.8.0.392.b08-7.fc39.ppc64le java-1.8.0-openjdk-headless-1:1.8.0.392.b08-7.fc39.ppc64le java-17-openjdk-headless-1:17.0.10.0.7-1.fc40.ppc64le javapackages-filesystem-6.2.0-5.fc40.noarch javapackages-tools-6.2.0-5.fc40.noarch jbigkit-libs-2.1-27.fc40.ppc64le jsoncpp-1.9.5-5.fc39.ppc64le junit-1:4.13.2-2.fc40.noarch kernel-headers-6.8.0-0.rc1.12.fc40.ppc64le lcms2-2.16-2.fc40.ppc64le libICE-1.1.1-1.fc40.ppc64le libICE-devel-1.1.1-1.fc40.ppc64le libSM-1.2.4-1.fc40.ppc64le libSM-devel-1.2.4-1.fc40.ppc64le libX11-1.8.7-1.fc40.ppc64le libX11-common-1.8.7-1.fc40.noarch libX11-devel-1.8.7-1.fc40.ppc64le libX11-xcb-1.8.7-1.fc40.ppc64le libXau-1.0.11-4.fc40.ppc64le libXau-devel-1.0.11-4.fc40.ppc64le libXcomposite-0.4.6-1.fc40.ppc64le libXcursor-1.2.1-5.fc40.ppc64le libXcursor-devel-1.2.1-5.fc40.ppc64le libXext-1.3.5-5.fc40.ppc64le libXext-devel-1.3.5-5.fc40.ppc64le libXfixes-6.0.1-1.fc40.ppc64le libXfixes-devel-6.0.1-1.fc40.ppc64le libXft-2.3.8-4.fc40.ppc64le libXft-devel-2.3.8-4.fc40.ppc64le libXi-1.8.1-3.fc40.ppc64le libXi-devel-1.8.1-3.fc40.ppc64le libXinerama-1.1.5-4.fc40.ppc64le libXinerama-devel-1.1.5-4.fc40.ppc64le libXrandr-1.5.4-1.fc40.ppc64le libXrandr-devel-1.5.4-1.fc40.ppc64le libXrender-0.9.11-4.fc40.ppc64le libXrender-devel-0.9.11-4.fc40.ppc64le libXt-1.3.0-1.fc40.ppc64le libXt-devel-1.3.0-1.fc40.ppc64le libXtst-1.2.4-4.fc40.ppc64le libXv-1.0.12-1.fc40.ppc64le libXv-devel-1.0.12-1.fc40.ppc64le libXxf86vm-1.1.5-4.fc40.ppc64le libasan-14.0.1-0.3.fc40.ppc64le libatomic-14.0.1-0.3.fc40.ppc64le libb2-0.98.1-9.fc39.ppc64le libblkid-devel-2.39.3-4.fc40.ppc64le libdrm-2.4.120-1.fc40.ppc64le libedit-3.1-48.20230828cvs.fc40.ppc64le libedit-devel-3.1-48.20230828cvs.fc40.ppc64le libevdev-1.13.1-2.fc39.ppc64le libffi-devel-3.4.4-5.fc40.ppc64le libfontenc-1.1.7-1.fc40.ppc64le libgfortran-14.0.1-0.3.fc40.ppc64le libglvnd-1:1.7.0-1.fc40.ppc64le libglvnd-core-devel-1:1.7.0-1.fc40.ppc64le libglvnd-devel-1:1.7.0-1.fc40.ppc64le libglvnd-egl-1:1.7.0-1.fc40.ppc64le libglvnd-gles-1:1.7.0-1.fc40.ppc64le libglvnd-glx-1:1.7.0-1.fc40.ppc64le libglvnd-opengl-1:1.7.0-1.fc40.ppc64le libgudev-238-2.fc39.ppc64le libicu-73.2-3.fc40.ppc64le libicu-devel-73.2-3.fc40.ppc64le libinput-1.25.0-1.fc40.ppc64le libjpeg-turbo-2.1.4-5.fc40.ppc64le liblerc-4.0.0-4.fc39.ppc64le libmng-2.0.3-19.fc39.ppc64le libmount-devel-2.39.3-4.fc40.ppc64le libmpc-1.3.1-3.fc39.ppc64le libnauty-2.8.8-1.fc40.ppc64le libpng-2:1.6.40-1.fc40.ppc64le libpng-devel-2:1.6.40-1.fc40.ppc64le libproxy-0.5.3-3.fc40.ppc64le libquadmath-14.0.1-0.3.fc40.ppc64le libselinux-devel-3.6-2.fc40.ppc64le libsepol-devel-3.6-1.fc40.ppc64le libstdc++-devel-14.0.1-0.3.fc40.ppc64le libstdc++-static-14.0.1-0.3.fc40.ppc64le libtiff-4.5.0-3.fc40.ppc64le libtool-ltdl-2.4.7-10.fc40.ppc64le libubsan-14.0.1-0.3.fc40.ppc64le libuuid-devel-2.39.3-4.fc40.ppc64le libuv-1:1.47.0-3.fc40.ppc64le libwacom-2.9.0-1.fc40.ppc64le libwacom-data-2.9.0-1.fc40.noarch libwayland-client-1.22.0-2.fc39.ppc64le libwayland-server-1.22.0-2.fc39.ppc64le libwebp-1.3.2-4.fc40.ppc64le libxcb-1.16-2.fc40.ppc64le libxcb-devel-1.16-2.fc40.ppc64le libxcrypt-devel-4.4.36-4.fc40.ppc64le libxkbcommon-1.6.0-2.fc40.ppc64le libxkbcommon-x11-1.6.0-2.fc40.ppc64le libxml2-devel-2.12.4-1.fc40.ppc64le libxshmfence-1.3.2-1.fc40.ppc64le lksctp-tools-1.0.19-4.fc39.ppc64le llvm-17.0.6-2.fc40.ppc64le llvm-devel-17.0.6-2.fc40.ppc64le llvm-googletest-17.0.6-2.fc40.ppc64le llvm-libs-17.0.6-2.fc40.ppc64le llvm-static-17.0.6-2.fc40.ppc64le llvm-test-17.0.6-2.fc40.ppc64le lua-5.4.6-3.fc39.ppc64le lua-filesystem-1.8.0-9.fc39.ppc64le lua-json-1.3.4-4.fc39.noarch lua-lpeg-1.0.2-11.fc39.ppc64le lua-posix-36.2.1-3.fc39.ppc64le lua-term-0.08-1.fc40.ppc64le make-1:4.4.1-2.fc39.ppc64le mesa-libEGL-24.0.0~rc2-4.fc40.ppc64le mesa-libGL-24.0.0~rc2-4.fc40.ppc64le mesa-libGLU-9.0.3-1.fc39.ppc64le mesa-libGLU-devel-9.0.3-1.fc39.ppc64le mesa-libgbm-24.0.0~rc2-4.fc40.ppc64le mesa-libglapi-24.0.0~rc2-4.fc40.ppc64le metis-5.1.0.3-3.fc40.ppc64le mkfontscale-1.2.2-4.fc39.ppc64le mockito-5.8.0-1.fc40.noarch mp-3.1.0-42.20200303git7fd4828.fc39.ppc64le mpdecimal-2.5.1-7.fc39.ppc64le mtdev-1.1.6-6.fc39.ppc64le ncurses-c++-libs-6.4-9.20240113.fc40.ppc64le ncurses-devel-6.4-9.20240113.fc40.ppc64le nettle-3.9.1-2.fc39.ppc64le nspr-4.35.0-17.fc40.ppc64le nss-3.96.1-1.fc40.ppc64le nss-softokn-3.96.1-1.fc40.ppc64le nss-softokn-freebl-3.96.1-1.fc40.ppc64le nss-sysinit-3.96.1-1.fc40.ppc64le nss-util-3.96.1-1.fc40.ppc64le objectweb-asm-9.6-1.fc40.noarch objenesis-3.3-4.fc40.noarch openblas-0.3.26-1.fc40.ppc64le openblas-openmp-0.3.26-1.fc40.ppc64le opentest4j-1.3.0-2.fc40.noarch pcre2-devel-10.42-2.fc40.ppc64le pcre2-utf16-10.42-2.fc40.ppc64le pcre2-utf32-10.42-2.fc40.ppc64le pixman-0.43.0-1.fc40.ppc64le procps-ng-4.0.4-1.fc40.ppc64le pyproject-rpm-macros-1.12.0-1.fc40.noarch python-pip-wheel-23.3.2-1.fc40.noarch python-rpm-macros-3.12-7.fc40.noarch python3-3.12.1-2.fc40.ppc64le python3-devel-3.12.1-2.fc40.ppc64le python3-libs-3.12.1-2.fc40.ppc64le python3-numpy-1:1.26.2-4.fc40.ppc64le python3-packaging-23.2-2.fc40.noarch python3-rpm-generators-14-8.fc40.noarch python3-rpm-macros-3.12-7.fc40.noarch python3-setuptools-68.2.2-1.fc40.noarch qt-1:4.8.7-74.fc39.ppc64le qt-common-1:4.8.7-74.fc39.noarch qt-devel-1:4.8.7-74.fc39.ppc64le qt-settings-39.1-3.fc40.noarch qt-x11-1:4.8.7-74.fc39.ppc64le qt5-qtbase-5.15.12-1.fc40.ppc64le qt5-qtbase-common-5.15.12-1.fc40.noarch qt5-qtbase-gui-5.15.12-1.fc40.ppc64le rhash-1.4.3-3.fc39.ppc64le scotch-7.0.4-2.fc40.ppc64le scotch-devel-7.0.4-2.fc40.ppc64le suitesparse-5.13.0-4.fc40.ppc64le sysprof-capture-devel-45.1-1.fc40.ppc64le tcl-1:8.6.13-1.fc40.ppc64le ttmkfdir-3.0.9-69.fc39.ppc64le tzdata-2023d-2.fc40.noarch tzdata-java-2023d-2.fc40.noarch unixODBC-2.3.12-2.fc40.ppc64le vim-filesystem-2:9.1.031-1.fc40.noarch xcb-util-0.4.1-3.fc39.ppc64le xcb-util-image-0.4.1-3.fc39.ppc64le xcb-util-keysyms-0.4.1-3.fc39.ppc64le xcb-util-renderutil-0.3.10-3.fc39.ppc64le xcb-util-wm-0.4.2-3.fc39.ppc64le xkeyboard-config-2.40-2.fc40.noarch xml-common-0.6.3-62.fc40.noarch xorg-x11-fonts-Type1-7.5-37.fc40.noarch xorg-x11-proto-devel-2023.2-3.fc40.noarch xz-devel-5.4.5-1.fc40.ppc64le zlib-ng-compat-devel-2.1.6-1.fc40.ppc64le Complete! Finish: build setup for seqan-1.4.2-53.fc40.src.rpm Start: rpmbuild seqan-1.4.2-53.fc40.src.rpm warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1706313600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.NWobCF + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf seqan-1.4.2 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/seqan-src-1.4.2.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd seqan-1.4.2 + rm -rf /builddir/build/BUILD/seqan-1.4.2-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/seqan-1.4.2-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (seqan-docpath.patch):' Patch #0 (seqan-docpath.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p0 --fuzz=0 patching file util/cmake/SeqAnBuildSystem.cmake + echo 'Patch #1 (seqan-exclude_splazers_fiona_tests.patch):' Patch #1 (seqan-exclude_splazers_fiona_tests.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p0 --fuzz=0 patching file core/apps/splazers/CMakeLists.txt patching file core/apps/fiona/CMakeLists.txt + echo 'Patch #2 (seqan-exclude_bstools_test.patch):' Patch #2 (seqan-exclude_bstools_test.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p0 --fuzz=0 patching file extras/apps/bs_tools/CMakeLists.txt patching file core/apps/samcat/CMakeLists.txt + find . -type f -name '*.h' -exec chmod 0644 '{}' ';' + find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';' + cp -p extras/apps/rep_sep/LICENSE LGPLv3+.txt + cp -p core/apps/rabema/LICENSE GPLv3+.txt + cp -p LICENSE BSD.txt + cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.kpGP8c ~/build/BUILD/seqan-1.4.2/build/Release ~/build/BUILD/seqan-1.4.2 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd seqan-1.4.2 + mkdir -p build/Release + pushd build/Release + SEQAN_OPT_FLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC' + export 'CXXFLAGS=-std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon' + CXXFLAGS='-std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon' + export 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fPIC' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fPIC' + cmake '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC' -DCMAKE_INSTALL_PREFIX:PATH=/usr -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_APP_VERSION:STRING=1.4.2 -DZLIB_INCLUDE_DIR:PATH=/usr/include '-DZLIB_LIBRARY:FILEPATH=-L/usr/lib64 -lz' -DBZIP2_INCLUDE_DIR:PATH=/usr/include '-DBZIP2_LIBRARY:FILEPATH=-L/usr/lib64 -lbz2' -DLEMON_INCLUDE_DIR:PATH=/usr/include '-DLEMON_LIBRARY:FILEPATH=-L/usr/lib64 -lemon' -DBoost_INCLUDE_DIR:PATH=/usr/include -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../.. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 14.0.1 -- The CXX compiler identification is GNU 14.0.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Initializing SeqAn Build System... -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring core CMake Deprecation Warning at core/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at core/apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps CMake Deprecation Warning at core/apps/dfi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/dfi -- Looking for include file execinfo.h -- Looking for include file execinfo.h - found -- Determined version is 1.4.2 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/dfi/CMakeLists.txt:70 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found version "3.12.1") CMake Deprecation Warning at core/apps/fiona/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/fiona -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") CMake Deprecation Warning at core/apps/mason/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/mason CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/mason/CMakeLists.txt:76 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/micro_razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/micro_razers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/micro_razers/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/pair_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/pair_align CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/pair_align/CMakeLists.txt:63 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/rabema/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/rabema CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/rabema/CMakeLists.txt:101 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/razers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/razers/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/razers2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/razers2 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/razers2/CMakeLists.txt:82 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/sak/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/sak CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/sak/CMakeLists.txt:78 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/sam2matrix/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/sam2matrix CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/sam2matrix/CMakeLists.txt:66 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/samcat/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/samcat CMake Deprecation Warning at core/apps/seqan_tcoffee/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/seqan_tcoffee CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/seqan_tcoffee/CMakeLists.txt:65 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/seqcons/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/seqcons CMake Deprecation Warning at core/apps/snp_store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/snp_store CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/snp_store/CMakeLists.txt:86 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/splazers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/splazers CMake Deprecation Warning at core/apps/stellar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/stellar CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/stellar/CMakeLists.txt:71 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at core/apps/tree_recon/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring core/apps/tree_recon CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/apps/tree_recon/CMakeLists.txt:65 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring extras CMake Deprecation Warning at extras/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at extras/apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps CMake Deprecation Warning at extras/apps/alf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/alf CMake Deprecation Warning at extras/apps/breakpoint_calculator/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/breakpoint_calculator CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/breakpoint_calculator/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/bs_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/bs_tools CMake Deprecation Warning at extras/apps/fx_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/fx_tools CMake Deprecation Warning at extras/apps/gustaf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/gustaf CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/gustaf/CMakeLists.txt:68 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/insegt/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/insegt CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/insegt/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/mason2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/mason2 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/mason2/CMakeLists.txt:155 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/ngs_roi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring sandbox/jagla/apps/ngs_roi CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/ngs_roi/CMakeLists.txt:101 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/param_chooser/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/param_chooser CMake Deprecation Warning at extras/apps/razers3/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/razers3 -- Performing Test CXX11_FOUND -- Performing Test CXX11_FOUND - Success -- Looking for BZ2_bzCompressInit in -L/usr/lib64 -lbz2 -- Looking for BZ2_bzCompressInit in -L/usr/lib64 -lbz2 - found CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/razers3/CMakeLists.txt:108 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/razers3/CMakeLists.txt:112 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/rep_sep/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/rep_sep CMake Deprecation Warning at extras/apps/searchjoin/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/searchjoin CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/searchjoin/CMakeLists.txt:69 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/seqan_flexbar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/seqan_flexbar CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/seqan_flexbar/CMakeLists.txt:92 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/sgip/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/sgip CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/sgip/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at extras/apps/variant_comp/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring extras/apps/variant_comp CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:223 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): extras/apps/variant_comp/CMakeLists.txt:65 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring docs CMake Deprecation Warning at docs/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring manual CMake Deprecation Warning at manual/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) -- Sphinx not found, not building sphinx manual as a test. -- Configuring sandbox CMake Deprecation Warning at sandbox/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring util/py_lib CMake Warning (dev) at util/py_lib/CMakeLists.txt:12 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Python nosetests ('import nose' failed), cannot add tests for seqan.dox -- Found Java: /usr/bin/java (found version "17.0.10") -- Configuring done (5.5s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_SKIP_INSTALL_RPATH SEQAN_APP_VERSION SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/seqan-1.4.2/build/Release + make -j1 all /usr/bin/cmake -S/builddir/build/BUILD/seqan-1.4.2 -B/builddir/build/BUILD/seqan-1.4.2/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-1.4.2/build/Release/CMakeFiles /builddir/build/BUILD/seqan-1.4.2/build/Release//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/CMakeFiles/seqan_core.dir/build.make core/CMakeFiles/seqan_core.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core /builddir/build/BUILD/seqan-1.4.2/build/Release/core/CMakeFiles/seqan_core.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/CMakeFiles/seqan_core.dir/build.make core/CMakeFiles/seqan_core.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/CMakeFiles/seqan_core.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 0%] Built target seqan_core make -f core/apps/dfi/CMakeFiles/dfi.dir/build.make core/apps/dfi/CMakeFiles/dfi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/dfi /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/dfi/CMakeFiles/dfi.dir/build.make core/apps/dfi/CMakeFiles/dfi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 1%] Building CXX object core/apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/dfi && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -MF CMakeFiles/dfi.dir/dfi.cpp.o.d -o CMakeFiles/dfi.dir/dfi.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:28: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:274:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 274 | struct LessSubstringEnd : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:298:27: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 298 | struct LessRange : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:315:25: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 315 | struct LessLex : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1871 | TSize size = _sortWotdBucket( /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~ 1873 | value(it).range.i1, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 800 | TSize childNode = _wotdEvaluate(it); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1977 | while (goDown(it)) ; /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 537 | goBegin(it); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:847:68: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 847 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:848:64: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 848 | case 1: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:849:58: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 849 | case 2: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = unsigned char; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:854:69: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 854 | case 0: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:855:65: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 855 | case 1: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:856:59: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 856 | case 2: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = unsigned char; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:861:71: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 861 | case 0: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:862:67: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 862 | case 1: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; TBeginPos = long unsigned int; TEndPos = long unsigned int; TSize = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:1871:32: required from ‘typename seqan::Size > >::Type seqan::_wotdEvaluate(const Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = TopDown >; typename Size > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1871 | TSize size = _sortWotdBucket( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^ 1872 | index, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~ 1873 | value(it).range.i1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~ 1874 | w1 & index.BITMASK1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 1875 | repLength(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:800:34: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = Dfi; TSpec = ParentLinks; TDfsOrder = Preorder_; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 800 | TSize childNode = _wotdEvaluate(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexWotd > >; TSpec = ParentLinks]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:1977:17: required from ‘void seqan::goBegin(Iter, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = IndexWotd >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1977 | while (goDown(it)) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:537:9: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | goBegin(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:863:61: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 863 | case 2: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Owner<> >; TPredHull = PredMinFreq; TPred = PredMaxFreq; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:847:68: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 847 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Owner<> >; TPredHull = PredMinFreq; TPred = PredMaxFreq; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:847:68: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 847 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinFreq; TPred = PredMaxFreq; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:848:64: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 848 | case 1: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinFreq; TPred = PredMaxFreq; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:848:64: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 848 | case 1: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinFreq; TPred = PredMaxFreq; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:849:58: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 849 | case 2: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinFreq; TPred = PredMaxFreq; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinFreq; TPred = PredMaxFreq; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:849:58: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 849 | case 2: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Owner<> >; TPredHull = PredMinSupp; TPred = PredEmerging; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = unsigned char; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:854:69: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 854 | case 0: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Owner<> >; TPredHull = PredMinSupp; TPred = PredEmerging; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = unsigned char; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:854:69: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 854 | case 0: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinSupp; TPred = PredEmerging; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:855:65: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 855 | case 1: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinSupp; TPred = PredEmerging; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:855:65: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 855 | case 1: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinSupp; TPred = PredEmerging; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:856:59: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 856 | case 2: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinSupp; TPred = PredEmerging; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinSupp; TPred = PredEmerging; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinSupp; TPred = PredEmerging; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:856:59: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 856 | case 2: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.growthRate, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Owner<> >; TPredHull = PredMinAllSupp; TPred = PredEntropy; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = unsigned char; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:861:71: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 861 | case 0: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Owner<> >; TPredHull = PredMinAllSupp; TPred = PredEntropy; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = unsigned char; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:861:71: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 861 | case 0: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinAllSupp; TPred = PredEntropy; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:862:67: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 862 | case 1: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinAllSupp; TPred = PredEntropy; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:862:67: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 862 | case 1: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘typename seqan::Size, seqan::IndexWotd > > >::Type seqan::_sortFirstWotdBucket(Index, IndexWotd > >&) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; typename Size, IndexWotd > > >::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2021:31: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2021 | size = _sortFirstWotdBucket(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinAllSupp; TPred = PredEntropy; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:863:61: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 863 | case 2: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:302:66: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 302 | *(saBeg + (*(boundBeg + ord))++) = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In instantiation of ‘TSize seqan::_sortWotdBucket(Index, IndexWotd > >&, TBeginPos, TEndPos, TSize) [with TText = String, Alloc<> >; TSpec = Owner<>; TPredHull = PredMinAllSupp; TPred = PredEntropy; TBeginPos = int; TEndPos = long unsigned int; TSize = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:2024:26: required from ‘void seqan::_wotdCreateFirstLevel(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2024 | size = _sortWotdBucket(index, 0, length(indexSA(index)), 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:615:24: required from ‘bool seqan::indexCreate(Index > >&, WotdDir, Default) [with TText = StringSet, Alloc<> >, Owner<> >; TPredHull = PredMinAllSupp; TPred = PredEntropy; WotdDir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 615 | _wotdCreateFirstLevel(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexWotd >; TFibre = FibreDir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:363:15: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = Dfi]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 363 | indexRequire(index, WotdDir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexWotd > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:536:8: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinAllSupp; TPred = PredEntropy; TAlphabet = seqan::SimpleType; TParamPredHull = double; TParamPred = double; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 536 | TIter it(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:863:61: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 863 | case 2: return runDFI (getArgumentValues(parser, 0), options.minSupp, options.entropy, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:448:111: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 448 | *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:451:82: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 451 | *(saBeg + index.sentinelBound++) = *itSA; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:257:13: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 257 | assignSeq(seqs[ds[s] + i], multiFasta[i], format); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:504:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 504 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:848:64: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 848 | case 1: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:257:13: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 257 | assignSeq(seqs[ds[s] + i], multiFasta[i], format); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:504:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = seqan::SimpleType; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 504 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:849:58: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | case 2: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:845:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 845 | switch (options.alphabet) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:851:17: note: here 851 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:852:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 852 | switch (options.alphabet) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi/dfi.cpp:858:17: note: here 858 | case 2: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 1%] Linking CXX executable ../../../bin/dfi cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/dfi && /usr/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/dfi.dir/dfi.cpp.o -o ../../../bin/dfi -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 1%] Built target dfi make -f core/apps/fiona/CMakeFiles/compute_gain.dir/build.make core/apps/fiona/CMakeFiles/compute_gain.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona/CMakeFiles/compute_gain.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/fiona/CMakeFiles/compute_gain.dir/build.make core/apps/fiona/CMakeFiles/compute_gain.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 3%] Building CXX object core/apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o -MF CMakeFiles/compute_gain.dir/compute_gain.cpp.o.d -o CMakeFiles/compute_gain.dir/compute_gain.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:2: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:10: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = Stats*; TParam = Stats]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Stats*; TParam = Stats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:605:23: required from ‘void seqan::_arrayConstructCopyDefault(TSource1, TSource2, TTarget) [with TTarget = Stats*; TSource1 = Stats*; TSource2 = Stats*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 605 | valueConstruct(target_begin, getValue(source_begin)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1420:31: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, False) [with TValueSource = Stats; TValueTarget = Stats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1420 | _arrayConstructCopyDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = Stats; TValueTarget = Stats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:843:11: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 843 | resize(stats, options.numThreads); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:97:8: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> > >::Align(const seqan::Align, seqan::Alloc<> > >&)’ is deprecated [-Wdeprecated-copy] 97 | struct Stats | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:89: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:97:8: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> > >::Align(const seqan::Align, seqan::Alloc<> > >&)’ is deprecated [-Wdeprecated-copy] 97 | struct Stats | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:5: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘Stats::Stats(const Stats&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> > >; TValue = const seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = String, Alloc<> >; TTargetSpec = Alloc<>; TValue = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = String, Alloc<> >; TString2 = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> > >; TValue = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:1032:20: required from ‘typename seqan::EnableIf::Type, seqan::Tag >::Type, typename seqan::IsSameType::Type, seqan::Tag >::Type>::Type, int>::Type seqan::read2(StringSet&, StringSet&, RecordReader >&, const TTag&) [with TIdString = String >; TIdSpec = Owner<>; TSeqString = String, Alloc<> >; TSeqSpec = Owner<>; TFile = std::basic_fstream; TSpec = void; TTag = Tag; typename EnableIf::Type, Tag >::Type, typename IsSameType::Type, Tag >::Type>::Type, int>::Type = int; typename Or::Type, Tag >::Type, typename IsSameType::Type, Tag >::Type>::Type = True; typename IsSameType::Type, Tag >::Type = True; typename RemoveConst_::Type = Tag; typename IsSameType::Type, Tag >::Type = False]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1032 | appendValue(sequences, seq); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/compute_gain.cpp:809:14: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 809 | if (read2(ids, seqs, readerGenome, Fasta()) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 3%] Linking CXX executable ../../../bin/compute_gain cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/compute_gain.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/compute_gain.dir/compute_gain.cpp.o -o ../../../bin/compute_gain -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 3%] Built target compute_gain make -f core/apps/fiona/CMakeFiles/fiona.dir/build.make core/apps/fiona/CMakeFiles/fiona.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona/CMakeFiles/fiona.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/fiona/CMakeFiles/fiona.dir/build.make core/apps/fiona/CMakeFiles/fiona.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 4%] Building CXX object core/apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -MF CMakeFiles/fiona.dir/fiona.cpp.o.d -o CMakeFiles/fiona.dir/fiona.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:119: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:103: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1687:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1687 | struct LessOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1705:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1705 | struct LessPositionOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp: In function ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4212:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4212 | if (options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4215:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4215 | Dna5String tmp; | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4235:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4235 | if (options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4238:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4238 | double experrreads = expectedValueTheoretical(options.expectedTheoretical, readLengthHist, options.genomeLength, options.errorrate); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4413:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4413 | if (options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4416:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4416 | if (options.errorrate != 0 && options.wovsum != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4461:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4461 | if (options.verbosity >= 1) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:116: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/profiling.h:81:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 81 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4463:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 4463 | SEQAN_PROTIMESTART(search); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4684:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 4684 | for (unsigned i = 0; i < length(store.readSeqStore); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4689:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 4689 | TFionaQgramIndex qgramIndex(prefixes); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4852:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4852 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4854:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4854 | if (inTerm && options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5027:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5027 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5032:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5032 | resize(store.readSeqStore, readCount); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5479:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5479 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5483:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5483 | bool autoCycles = (options.cycles == 0 || options.cycles == 1000); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5486:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5486 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/profiling.h:81:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 81 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5489:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 5489 | SEQAN_PROTIMESTART(correction); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5495:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5495 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5497:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5497 | if (!loadReadsNoNames(store, options.inputFilename, options)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5561:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5561 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5563:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5563 | options.autolevel = (options.fromLevel <= 1); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5671:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5671 | if (res != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5674 | if (options.verbosity >= 1 && options.cycles > 1) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:132: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints, Tag) [with TSA = String >, Alloc<> >; TString = Segment, Alloc<> >, InfixSegment>; TSpec = Owner<>; TShape = Shape, UngappedShape<10> >; TDir = String >; TBucketMap = Nothing; TWithConstraints = True; TStepSize = long unsigned int; TParallelTag = Parallel_]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4761:30: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: 4761 | _qgramFillSuffixArray(indexSA(qgramIndex), indexText(qgramIndex), indexShape(qgramIndex), indexDir(qgramIndex), qgramIndex.bucketMap, getStepSize(qgramIndex), True(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h:438:61: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | sa[atomicPostInc(*bktPtr, parallelTag)] = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h:445:65: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 445 | sa[atomicPostInc(*bktPtr, parallelTag)] = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h:472:65: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 472 | sa[atomicPostInc(*bktPtr, parallelTag)] = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:116, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h: In instantiation of ‘void seqan::posLocalize(TResult&, const Pair&, const String&) [with TResult = Pair >; TSize = long unsigned int; TSpec = Alloc<>; T1 = unsigned int; T2 = short unsigned int; TPack = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:754:16: required from ‘typename seqan::Suffix::Type seqan::suffix(StringSet&, const TPosition&) [with TString = String, Alloc<> >; TSpec = Owner<>; TPosition = Pair >; typename Suffix::Type = Segment, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 754 | posLocalize(lPos, pos, stringSetLimits(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4918:43: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4918 | std::cerr << prefix(suffix(store.readSeqStore, front(indexSA(myIndex))), QGRAM_LENGTH) << " - "; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:699:12: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 699 | result = pos; | ~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:101: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4686:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4686 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:126: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:127: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:103:8: warning: implicitly-declared ‘constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)’ is deprecated [-Wdeprecated-copy] 103 | struct VertexSA : public VertexEsa | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:125: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:290:17: note: because ‘seqan::VertexEsa’ has user-provided ‘seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long unsigned int]’ 290 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: synthesized method ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ first required here 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = const seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagLimit_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >*>, InfixSegment>, Array<4> >; TValue = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:3625:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 3625 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4944:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 4944 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4686:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 4686 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2774:10: required from ‘void seqan::goNextImpl(Iter > > >&, VSTreeIteratorTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2774 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2052:13: required from ‘void seqan::goNext(Iter >&, TTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >; TTraits = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2052 | goNextImpl(it, traits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2047:9: required from ‘void seqan::goNext(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2047 | goNext(it, typename GetVSTreeIteratorTraits< Iter > >::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:3526:19: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3526 | goNext(iter); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4944:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4944 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = const seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagLimit_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >*>, InfixSegment>, Array<4> >; TValue = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:3625:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 3625 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4944:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 4944 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = long unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:842:19: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 842 | resize(kmer, length(shape), (TValue)x); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1958:22: required from ‘unsigned int applyReadErrorCorrections(const seqan::String&, seqan::String&, TReadStore&, FionaOptions&) [with TCorrection = CorrectionIndelPos; TValue = unsigned int; TReadStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1958 | erase(store.readSeqStore[readId], possibleCorrections[correction].errorPos, possibleCorrections[correction].errorPos + possibleCorrections[correction].indelLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5019:46: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5019 | totalCorrections = applyReadErrorCorrections(correctionList,firstCorrectionForRead,store,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:129: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h: In instantiation of ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = Range >*>; TText = StringSet, Alloc<> >, Owner<> >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:350:15: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 350 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1958:22: required from ‘unsigned int applyReadErrorCorrections(const seqan::String&, seqan::String&, TReadStore&, FionaOptions&) [with TCorrection = CorrectionIndelPos; TValue = unsigned int; TReadStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1958 | erase(store.readSeqStore[readId], possibleCorrections[correction].errorPos, possibleCorrections[correction].errorPos + possibleCorrections[correction].indelLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5019:46: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5019 | totalCorrections = applyReadErrorCorrections(correctionList,firstCorrectionForRead,store,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:98: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = Range >*>; TText = StringSet, Alloc<> >, Owner<> >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(Pipe&, TValue&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>; TSpec = Counter; TValue = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>, Counter>; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:386:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 386 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 387 | renamer, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 388 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:619:14: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 619 | Ref_ = *me; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:65: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 324 | TNames_Sliced names_sliced; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::pop(TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:925:24: required from ‘void seqan::Pool::pop(TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 925 | reader->pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1159:15: required from ‘void seqan::pop(Pool&, TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1159 | me.pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:926:18: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 926 | Ref_ = *cur; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:349:104: required from ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 349 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:349:104: required from ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 349 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:349:104: required from ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 349 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, long unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:106: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 341 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 352 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew7NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h: In instantiation of ‘TResult seqan::_skew7NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:335:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 148 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 247 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 259 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:124:27: required from ‘bool seqan::CompareSkewDCStream::operator()(const seqan::SkewDCStream&, const seqan::SkewDCStream&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 124 | if (a.i.i3[i] < b.i.i3[i]) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:307:23: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 307 | if (!streamGreater(inValue[stream],inValue[rank[right]])) break; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: required from ‘seqan::Pipe, seqan::Merger7>& seqan::Pipe, seqan::Merger7>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 319 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:440:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 440 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_counter.h:105:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >, seqan::Skew7>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 105 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:620:9: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew3NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew3NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h: In instantiation of ‘TResult seqan::_skew3NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TFunctor = seqan::filterI2 >, long unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_lss.h:415:29: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:241:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 86 | o2.i2[0] = (*nameIn).i2; ++nameIn; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:301:6: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 301 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 3; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 3, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 4; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 1; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 1, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 5; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 2; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 2, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:142:117: warning: this statement may fall through [-Wimplicit-fallthrough=] 142 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:144:9: note: here 144 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:145:118: warning: this statement may fall through [-Wimplicit-fallthrough=] 145 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:147:9: note: here 147 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:149:103: warning: this statement may fall through [-Wimplicit-fallthrough=] 149 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:151:9: note: here 151 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:152:119: warning: this statement may fall through [-Wimplicit-fallthrough=] 152 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:154:9: note: here 154 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:156:105: warning: this statement may fall through [-Wimplicit-fallthrough=] 156 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:158:9: note: here 158 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:121: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 4, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 4, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 5, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 5, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:279:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:289:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple, Tag > >; TLess = MergeStreamComparer, Tuple, Tag >, _skew3ExtendComp, Tuple, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew3NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew7NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26, inlined from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In constructor ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, 7, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, 7, BitPacked<> >, Tag >, _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 4%] Linking CXX executable ../../../bin/fiona cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/fiona.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/fiona.dir/fiona.cpp.o -o ../../../bin/fiona -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 4%] Built target fiona make -f core/apps/fiona/CMakeFiles/fiona_illumina.dir/build.make core/apps/fiona/CMakeFiles/fiona_illumina.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona/CMakeFiles/fiona_illumina.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/fiona/CMakeFiles/fiona_illumina.dir/build.make core/apps/fiona/CMakeFiles/fiona_illumina.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 4%] Building CXX object core/apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona && /usr/bin/g++ -DFIONA_ILLUMINA -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -MF CMakeFiles/fiona_illumina.dir/fiona.cpp.o.d -o CMakeFiles/fiona_illumina.dir/fiona.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:119: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:103: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1687:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1687 | struct LessOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1705:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1705 | struct LessPositionOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp: In function ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4212:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4212 | if (options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4215:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4215 | Dna5String tmp; | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4235:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4235 | if (options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4238:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4238 | double experrreads = expectedValueTheoretical(options.expectedTheoretical, readLengthHist, options.genomeLength, options.errorrate); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4413:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4413 | if (options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4416:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4416 | if (options.errorrate != 0 && options.wovsum != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4461:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4461 | if (options.verbosity >= 1) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:116: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/profiling.h:81:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 81 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4463:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 4463 | SEQAN_PROTIMESTART(search); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4684:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 4684 | for (unsigned i = 0; i < length(store.readSeqStore); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4689:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 4689 | TFionaQgramIndex qgramIndex(prefixes); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4852:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4852 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4854:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4854 | if (inTerm && options.verbosity >= 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5027:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5027 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5032:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5032 | resize(store.readSeqStore, readCount); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5479:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5479 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5483:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5483 | bool autoCycles = (options.cycles == 0 || options.cycles == 1000); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5486:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5486 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/profiling.h:81:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 81 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5489:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 5489 | SEQAN_PROTIMESTART(correction); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5495:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5495 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5497:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5497 | if (!loadReadsNoNames(store, options.inputFilename, options)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5561:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5561 | if (options.verbosity >= 1) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5563:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5563 | options.autolevel = (options.fromLevel <= 1); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5671:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 5671 | if (res != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 5674 | if (options.verbosity >= 1 && options.cycles > 1) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:132: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints, Tag) [with TSA = String >, Alloc<> >; TString = Segment, Alloc<> >, InfixSegment>; TSpec = Owner<>; TShape = Shape, UngappedShape<10> >; TDir = String >; TBucketMap = Nothing; TWithConstraints = True; TStepSize = long unsigned int; TParallelTag = Parallel_]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4761:30: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: 4761 | _qgramFillSuffixArray(indexSA(qgramIndex), indexText(qgramIndex), indexShape(qgramIndex), indexDir(qgramIndex), qgramIndex.bucketMap, getStepSize(qgramIndex), True(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5674:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h:438:61: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | sa[atomicPostInc(*bktPtr, parallelTag)] = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h:445:65: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 445 | sa[atomicPostInc(*bktPtr, parallelTag)] = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/index_qgram_parallel.h:472:65: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 472 | sa[atomicPostInc(*bktPtr, parallelTag)] = localPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:116, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h: In instantiation of ‘void seqan::posLocalize(TResult&, const Pair&, const String&) [with TResult = Pair >; TSize = long unsigned int; TSpec = Alloc<>; T1 = unsigned int; T2 = short unsigned int; TPack = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:754:16: required from ‘typename seqan::Suffix::Type seqan::suffix(StringSet&, const TPosition&) [with TString = String, Alloc<> >; TSpec = Owner<>; TPosition = Pair >; typename Suffix::Type = Segment, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 754 | posLocalize(lPos, pos, stringSetLimits(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4918:43: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4918 | std::cerr << prefix(suffix(store.readSeqStore, front(indexSA(myIndex))), QGRAM_LENGTH) << " - "; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:699:12: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 699 | result = pos; | ~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:101: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4686:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4686 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:126: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:127: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:103:8: warning: implicitly-declared ‘constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)’ is deprecated [-Wdeprecated-copy] 103 | struct VertexSA : public VertexEsa | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:125: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:290:17: note: because ‘seqan::VertexEsa’ has user-provided ‘seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long unsigned int]’ 290 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: synthesized method ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ first required here 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = const seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagLimit_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >*>, InfixSegment>, Array<4> >; TValue = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:3625:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 3625 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4944:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 4944 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4686:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 4686 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2774:10: required from ‘void seqan::goNextImpl(Iter > > >&, VSTreeIteratorTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2774 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2052:13: required from ‘void seqan::goNext(Iter >&, TTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >; TTraits = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2052 | goNextImpl(it, traits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2047:9: required from ‘void seqan::goNext(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2047 | goNext(it, typename GetVSTreeIteratorTraits< Iter > >::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:3526:19: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3526 | goNext(iter); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4944:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4944 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = const seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagLimit_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >*>, InfixSegment>, Array<4> >; TValue = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:3625:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 3625 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4944:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 4944 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = long unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:842:19: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 842 | resize(kmer, length(shape), (TValue)x); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1958:22: required from ‘unsigned int applyReadErrorCorrections(const seqan::String&, seqan::String&, TReadStore&, FionaOptions&) [with TCorrection = CorrectionIndelPos; TValue = unsigned int; TReadStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1958 | erase(store.readSeqStore[readId], possibleCorrections[correction].errorPos, possibleCorrections[correction].errorPos + possibleCorrections[correction].indelLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5019:46: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5019 | totalCorrections = applyReadErrorCorrections(correctionList,firstCorrectionForRead,store,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:129: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h: In instantiation of ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = Range >*>; TText = StringSet, Alloc<> >, Owner<> >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:350:15: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 350 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TSize = int; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TBeginPosition = short unsigned int; TEndPosition = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:1958:22: required from ‘unsigned int applyReadErrorCorrections(const seqan::String&, seqan::String&, TReadStore&, FionaOptions&) [with TCorrection = CorrectionIndelPos; TValue = unsigned int; TReadStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1958 | erase(store.readSeqStore[readId], possibleCorrections[correction].errorPos, possibleCorrections[correction].errorPos + possibleCorrections[correction].indelLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5019:46: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5019 | totalCorrections = applyReadErrorCorrections(correctionList,firstCorrectionForRead,store,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:98: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = Range >*>; TText = StringSet, Alloc<> >, Owner<> >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(Pipe&, TValue&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>; TSpec = Counter; TValue = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>, Counter>; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:386:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 386 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 387 | renamer, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 388 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:619:14: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 619 | Ref_ = *me; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:65: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 324 | TNames_Sliced names_sliced; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::pop(TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:925:24: required from ‘void seqan::Pool::pop(TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 925 | reader->pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1159:15: required from ‘void seqan::pop(Pool&, TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1159 | me.pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:926:18: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 926 | Ref_ = *cur; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:349:104: required from ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 349 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:349:104: required from ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 349 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:349:104: required from ‘void seqan::assign(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 349 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/sequence/iterator_range.h:359:11: required from ‘void seqan::operator<<(Range&, Pipe&) [with TIterator = Pair >*; TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TPipeSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 359 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, long unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:106: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 341 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 352 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = short unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew7NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h: In instantiation of ‘TResult seqan::_skew7NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:335:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 148 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 247 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 259 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:124:27: required from ‘bool seqan::CompareSkewDCStream::operator()(const seqan::SkewDCStream&, const seqan::SkewDCStream&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 124 | if (a.i.i3[i] < b.i.i3[i]) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:307:23: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 307 | if (!streamGreater(inValue[stream],inValue[rank[right]])) break; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: required from ‘seqan::Pipe, seqan::Merger7>& seqan::Pipe, seqan::Merger7>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 319 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:440:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 440 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_counter.h:105:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >, seqan::Skew7>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 105 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:620:9: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew3NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew3NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h: In instantiation of ‘TResult seqan::_skew3NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TFunctor = seqan::filterI2 >, long unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_lss.h:415:29: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:241:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 86 | o2.i2[0] = (*nameIn).i2; ++nameIn; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:301:6: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 301 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 3; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 3, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 4; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 1; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 1, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 5; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 2; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 2, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/../../extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:422:16: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 422 | TBase(_index) {} /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:4925:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 4925 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:5592:44: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 5592 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:142:117: warning: this statement may fall through [-Wimplicit-fallthrough=] 142 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:144:9: note: here 144 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:145:118: warning: this statement may fall through [-Wimplicit-fallthrough=] 145 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:147:9: note: here 147 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:149:103: warning: this statement may fall through [-Wimplicit-fallthrough=] 149 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:151:9: note: here 151 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:152:119: warning: this statement may fall through [-Wimplicit-fallthrough=] 152 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:154:9: note: here 154 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:156:105: warning: this statement may fall through [-Wimplicit-fallthrough=] 156 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:158:9: note: here 158 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64, from /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona/fiona.cpp:121: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 4, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 4, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 5, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 5, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:279:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:289:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple, Tag > >; TLess = MergeStreamComparer, Tuple, Tag >, _skew3ExtendComp, Tuple, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew3NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew7NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26, inlined from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In constructor ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, 7, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, 7, BitPacked<> >, Tag >, _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 6%] Linking CXX executable ../../../bin/fiona_illumina cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/fiona_illumina.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/fiona_illumina.dir/fiona.cpp.o -o ../../../bin/fiona_illumina -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 6%] Built target fiona_illumina make -f core/apps/mason/CMakeFiles/mason.dir/build.make core/apps/mason/CMakeFiles/mason.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/mason /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/mason /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/mason/CMakeFiles/mason.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/mason/CMakeFiles/mason.dir/build.make core/apps/mason/CMakeFiles/mason.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 8%] Building CXX object core/apps/mason/CMakeFiles/mason.dir/mason.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/mason && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/mason/CMakeFiles/mason.dir/mason.cpp.o -MF CMakeFiles/mason.dir/mason.cpp.o.d -o CMakeFiles/mason.dir/mason.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:39: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:90: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1189 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_anchor.h:465:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 465 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:628:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = String >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 628 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2582:18: required from ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2582 | insertGap(gaps, insPos - rBegin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1565:36: required from ‘int simulateReadsMain(seqan::FragmentStore&, TRNG&, const TOptions&, const ModelParameters&) [with TRNG = seqan::Rng; TReadsTag = seqan::Tag; TOptions = Options >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1565 | convertMatchesToGlobalAlignment(fragmentStore, Score(), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:608:28: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 608 | ret = simulateReadsMain(fragmentStore, rng, options, modelParameters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:75: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2091:19: required from ‘typename seqan::Size::Type seqan::reserve(T&, const TSize&) [with T = String, Alloc<> >; TSize = long unsigned int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2091 | return reserve(me, new_capacity, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:478:12: required from ‘int writeRandomSequence(TRNG&, size_t, const seqan::CharString&, const TOptions&) [with TRNG = seqan::Rng; TOptions = Options >; size_t = long unsigned int; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 478 | reserve(randomSequence, length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:568:38: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 568 | int ret = writeRandomSequence(rng, options.randomSourceLength, referenceFilename, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1385:31: required from ‘int simulateReadsMain(seqan::FragmentStore&, TRNG&, const TOptions&, const ModelParameters&) [with TRNG = seqan::Rng; TReadsTag = seqan::Tag; TOptions = Options >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1385 | String read = infix(haplotypeContigsCopy[inst.contigId], inst.beginPos, inst.endPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:608:28: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 608 | ret = simulateReadsMain(fragmentStore, rng, options, modelParameters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:700:14: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 700 | write(fstrm, fragmentStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence_journaled/sequence_journaled.h:745:11: required from ‘void seqan::insert(String >&, TPos, const TString&) [with TValue = SimpleType; THostSpec = Alloc<>; TJournalSpec = SortedArray; TBufferSpec = Alloc<>; TString = String >; TPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 745 | append(journaledString._insertionBuffer, seq); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:944:19: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 944 | insert(haplotype[contigId], pos + delta, alt[allele]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2091:19: required from ‘typename seqan::Size::Type seqan::reserve(T&, const TSize&) [with T = String, Alloc<> >; TSize = unsigned int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2091 | return reserve(me, new_capacity, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1008:12: required from ‘void buildHaplotype(seqan::StringSet, seqan::Journaled > > >&, seqan::FragmentStore&, seqan::String >&, TRNG&, const Options&) [with TRNG = seqan::Rng]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1008 | reserve(buffer, options.haplotypeIndelRangeMax); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1322:27: required from ‘int simulateReadsMain(seqan::FragmentStore&, TRNG&, const TOptions&, const ModelParameters&) [with TRNG = seqan::Rng; TReadsTag = seqan::Tag; TOptions = Options >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1322 | buildHaplotype(haplotypeContigs, fragmentStore, snpSet, rng, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:608:28: required from ‘int simulateReads(TOptions, seqan::CharString, const TReadsTypeTag&) [with TOptions = Options >; TReadsTypeTag = seqan::Tag; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 608 | ret = simulateReadsMain(fragmentStore, rng, options, modelParameters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:116:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 116 | return simulateReads(options, referenceFilename, IlluminaReads()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence_journaled/sequence_journaled.h:745:11: required from ‘void seqan::insert(String >&, TPos, const TString&) [with TValue = SimpleType; THostSpec = Alloc<>; TJournalSpec = SortedArray; TBufferSpec = Alloc<>; TString = String >; TPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 745 | append(journaledString._insertionBuffer, seq); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:944:19: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 944 | insert(haplotype[contigId], pos + delta, alt[allele]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tempbuf.h:59, from /usr/include/c++/14/bits/stl_algo.h:69, from /usr/include/c++/14/algorithm:61, from /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.cpp:37: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Alloc<> >; TValue = ReadSimulationInstruction >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = ReadSimulationInstruction >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘int buildReadSimulationInstruction(seqan::String >&, TRNG&, const unsigned int&, const seqan::StringSet, THaplotypeSpec> >&, const seqan::String&, const size_t&, bool, const ModelParameters&, const Options&) [with TReadsTag = seqan::Tag; TRNG = seqan::Rng; THaplotypeSpec = seqan::Alloc<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1193:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551456’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘int buildReadSimulationInstruction(seqan::String >&, TRNG&, const unsigned int&, const seqan::StringSet, THaplotypeSpec> >&, const seqan::String&, const size_t&, bool, const ModelParameters&, const Options&) [with TReadsTag = seqan::Tag; TRNG = seqan::Rng; THaplotypeSpec = seqan::Alloc<>]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Alloc<> >; TValue = ReadSimulationInstruction >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = ReadSimulationInstruction >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘int buildReadSimulationInstruction(seqan::String >&, TRNG&, const unsigned int&, const seqan::StringSet, THaplotypeSpec> >&, const seqan::String&, const size_t&, bool, const ModelParameters&, const Options&) [with TReadsTag = seqan::Tag; TRNG = seqan::Rng; THaplotypeSpec = seqan::Alloc<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1193:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551456’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘int buildReadSimulationInstruction(seqan::String >&, TRNG&, const unsigned int&, const seqan::StringSet, THaplotypeSpec> >&, const seqan::String&, const size_t&, bool, const ModelParameters&, const Options&) [with TReadsTag = seqan::Tag; TRNG = seqan::Rng; THaplotypeSpec = seqan::Alloc<>]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Alloc<> >; TValue = ReadSimulationInstruction >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = ReadSimulationInstruction >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = ReadSimulationInstruction >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘int buildReadSimulationInstruction(seqan::String >&, TRNG&, const unsigned int&, const seqan::StringSet, THaplotypeSpec> >&, const seqan::String&, const size_t&, bool, const ModelParameters&, const Options&) [with TReadsTag = seqan::Tag<_LS454Reads>; TRNG = seqan::Rng; THaplotypeSpec = seqan::Alloc<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/mason/mason.h:1193:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551408’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘int buildReadSimulationInstruction(seqan::String >&, TRNG&, const unsigned int&, const seqan::StringSet, THaplotypeSpec> >&, const seqan::String&, const size_t&, bool, const ModelParameters&, const Options&) [with TReadsTag = seqan::Tag<_LS454Reads>; TRNG = seqan::Rng; THaplotypeSpec = seqan::Alloc<>]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 8%] Linking CXX executable ../../../bin/mason cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/mason && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason.dir/mason.cpp.o -o ../../../bin/mason -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 8%] Built target mason make -f core/apps/micro_razers/CMakeFiles/micro_razers.dir/build.make core/apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/micro_razers/CMakeFiles/micro_razers.dir/build.make core/apps/micro_razers/CMakeFiles/micro_razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 8%] Building CXX object core/apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o -MF CMakeFiles/micro_razers.dir/micro_razers.cpp.o.d -o CMakeFiles/micro_razers.dir/micro_razers.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:28, from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:662:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 662 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:691:49: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 691 | struct LessRNoEdistHLen : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:747:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 747 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:779:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 779 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/outputFormat.h:30, from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:38: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/outputFormat.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, TStringSet&, TShape&, TDir&, Nothing, TWithConstraints, TValue, MicroRNA) [with TSA = String >, Alloc<> >; TStringSet = StringSet >, Owner > >; TShape = Shape, UngappedShape<0> >; TDir = String >; TValue = unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1911:25: required from ‘void seqan::createQGramIndex(TIndex&, TValue, MicroRNA) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1911 | _qgramFillSuffixArray(sa, text, shape, dir, nothing, True(), prefixLen, MicroRNA()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2007:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 2007 | createQGramIndex(swiftIndex,options.rnaSeedLength,MicroRNA()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1845:71: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1845 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:56, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1847:68: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1847 | sa[dir[hash(shape, itText) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1855:79: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1855 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1857:80: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1857 | sa[dir[hashNext(shape, itText) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, TStringSet&, TShape&, TDir&, Nothing, TWithConstraints, TValue, MicroRNA) [with TSA = String >, Alloc<> >; TStringSet = StringSet >, Owner > >; TShape = Shape, UngappedShape<0> >; TDir = String >; TValue = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1922:25: required from ‘void seqan::createQGramIndex(TIndex&, TValue, MicroRNA) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1922 | _qgramFillSuffixArray(sa, text, shape, dir, nothing, False(),prefixLen, MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2007:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2007 | createQGramIndex(swiftIndex,options.rnaSeedLength,MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1845:71: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1845 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1847:68: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1847 | sa[dir[hash(shape, itText) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1855:79: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1855 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1857:80: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1857 | sa[dir[hashNext(shape, itText) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, const TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobalHamming) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobalHamming = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1378:35: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1378 | return matchVerify(m,inf,rseqNo,readSet,options,MicroRNA()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: initializing argument 2 of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, const RazerSOptions&, MicroRNA) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TSpec = RazerSSpec<>]’ 1276 | Segment inf, // potential match genome region | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, TStringSet&, TShape&, TDir&, Nothing, TWithConstraints, TValue, MicroRNA) [with TSA = String >, Alloc<> >; TStringSet = StringSet >, Owner > >; TShape = Shape, OneGappedShape>; TDir = String >; TValue = unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1911:25: required from ‘void seqan::createQGramIndex(TIndex&, TValue, MicroRNA) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: 1911 | _qgramFillSuffixArray(sa, text, shape, dir, nothing, True(), prefixLen, MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2007:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: 2007 | createQGramIndex(swiftIndex,options.rnaSeedLength,MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1276:40: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1845:71: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1845 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1847:68: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1847 | sa[dir[hash(shape, itText) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1855:79: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1855 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1857:80: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1857 | sa[dir[hashNext(shape, itText) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, TStringSet&, TShape&, TDir&, Nothing, TWithConstraints, TValue, MicroRNA) [with TSA = String >, Alloc<> >; TStringSet = StringSet >, Owner > >; TShape = Shape, OneGappedShape>; TDir = String >; TValue = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1922:25: required from ‘void seqan::createQGramIndex(TIndex&, TValue, MicroRNA) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1922 | _qgramFillSuffixArray(sa, text, shape, dir, nothing, False(),prefixLen, MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2007:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2007 | createQGramIndex(swiftIndex,options.rnaSeedLength,MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1845:71: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1845 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1847:68: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1847 | sa[dir[hash(shape, itText) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1855:79: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1855 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1857:80: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1857 | sa[dir[hashNext(shape, itText) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, TStringSet&, TShape&, TDir&, Nothing, TWithConstraints, TValue, MicroRNA) [with TSA = String >, Alloc<> >; TStringSet = StringSet >, Owner > >; TShape = Shape, GappedShape > >; TDir = String >; TValue = unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1911:25: required from ‘void seqan::createQGramIndex(TIndex&, TValue, MicroRNA) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1911 | _qgramFillSuffixArray(sa, text, shape, dir, nothing, True(), prefixLen, MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2007:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2007 | createQGramIndex(swiftIndex,options.rnaSeedLength,MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1845:71: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1845 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1847:68: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1847 | sa[dir[hash(shape, itText) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1855:79: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1855 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1857:80: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1857 | sa[dir[hashNext(shape, itText) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, TStringSet&, TShape&, TDir&, Nothing, TWithConstraints, TValue, MicroRNA) [with TSA = String >, Alloc<> >; TStringSet = StringSet >, Owner > >; TShape = Shape, GappedShape > >; TDir = String >; TValue = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1922:25: required from ‘void seqan::createQGramIndex(TIndex&, TValue, MicroRNA) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1922 | _qgramFillSuffixArray(sa, text, shape, dir, nothing, False(),prefixLen, MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2007:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2007 | createQGramIndex(swiftIndex,options.rnaSeedLength,MicroRNA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1845:71: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1845 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1847:68: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1847 | sa[dir[hash(shape, itText) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1855:79: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1855 | if (dir[h] != (TSize)-1) sa[dir[h]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1857:80: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1857 | sa[dir[hashNext(shape, itText) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1490:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1490 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:570:9: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 570 | reserve(reads.concat, length(reads.concat), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:158:19: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 158 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:162: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1716:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1716 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1716:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1716 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:76: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:5: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1459:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1459 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1490:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1490 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1491:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1491 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1716:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1716 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2306:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2306 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1716:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1716 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2309:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2309 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1459:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1459 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1685:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1685 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1685:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1685 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1685:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1685 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1474:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1474 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1492:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1492 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:612:11: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 612 | assignSeq(firstRead, multiFasta[0], format); // read the first sequence /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:562:14: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 562 | appendValue(reads, seq, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:158:19: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 158 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:18: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 793 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1497:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1497 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:182:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 182 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/razers.h:562:14: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 562 | appendValue(reads, seq, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:158:19: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 158 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:537:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 537 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:484:9: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 484 | resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:456:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 456 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:456:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 456 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:456:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 456 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /usr/include/c++/14/string:51: In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11, inlined from ‘void seqan::_parse_readShape(TFile&, TChar&, CharString&) [with TFile = std::basic_fstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:861:15, inlined from ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::basic_fstream; TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:1068:25, inlined from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:1342:26: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/micro_razers.cpp:39: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h: In function ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers/../razers/paramChooser.h:1043:10: note: ‘c’ declared here 1043 | char c = _streamGet(file); | ^ [ 9%] Building CXX object core/apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -MF CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o.d -o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/param_tabs.cpp [ 9%] Linking CXX executable ../../../bin/micro_razers cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/micro_razers.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/micro_razers.dir/micro_razers.cpp.o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -o ../../../bin/micro_razers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 9%] Built target micro_razers make -f core/apps/pair_align/CMakeFiles/pair_align.dir/build.make core/apps/pair_align/CMakeFiles/pair_align.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/pair_align /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/pair_align/CMakeFiles/pair_align.dir/build.make core/apps/pair_align/CMakeFiles/pair_align.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 11%] Building CXX object core/apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/pair_align && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o -MF CMakeFiles/pair_align.dir/pair_align.cpp.o.d -o CMakeFiles/pair_align.dir/pair_align.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:19: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:18: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:1892:17: required from ‘bool seqan::convertAlignment(const Graph >&, TMatrix&) [with TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = void; TSpec = const Tag; TMatrix = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 1892 | TStringSetStr str = label(g,it->second); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:897:22: required from ‘void seqan::write(TFile&, const Graph&, const TNames&, FastaFormat) [with TFile = _IO_FILE*; TSpec = Alignment, Alloc<> >, Dependent > >, void, const Tag >; TNames = StringSet > >; FastaFormat = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 897 | if (convertAlignment(g, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:131:14: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutputFormat, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score >; TSeqFile = std::__cxx11::basic_string; TMethod = unsigned int; TDiag = int; TOutputFormat = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 131 | write(strmWrite, gAlign, sequenceNames, FastaFormat()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:215:76: required from ‘void _initAlignParams(const Options&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 215 | pairwise_align >(sc, seqfile, method, low, high, banded, options.outputFormat, outfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:262:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: 262 | _initAlignParams(options, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:1892:17: required from ‘bool seqan::convertAlignment(const Graph >&, TMatrix&) [with TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = void; TSpec = const Tag; TMatrix = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1892 | TStringSetStr str = label(g,it->second); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:897:22: required from ‘void seqan::write(TFile&, const Graph&, const TNames&, FastaFormat) [with TFile = _IO_FILE*; TSpec = Alignment, Alloc<> >, Dependent > >, void, const Tag >; TNames = StringSet > >; FastaFormat = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 897 | if (convertAlignment(g, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:131:14: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutputFormat, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score >; TSeqFile = std::__cxx11::basic_string; TMethod = unsigned int; TDiag = int; TOutputFormat = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | write(strmWrite, gAlign, sequenceNames, FastaFormat()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:215:76: required from ‘void _initAlignParams(const Options&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 215 | pairwise_align >(sc, seqfile, method, low, high, banded, options.outputFormat, outfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:298:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 298 | _initAlignParams(options, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:1892:17: required from ‘bool seqan::convertAlignment(const Graph >&, TMatrix&) [with TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = void; TSpec = const Tag; TMatrix = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1892 | TStringSetStr str = label(g,it->second); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:897:22: required from ‘void seqan::write(TFile&, const Graph&, const TNames&, FastaFormat) [with TFile = _IO_FILE*; TSpec = Alignment, Alloc<> >, Dependent > >, void, const Tag >; TNames = StringSet > >; FastaFormat = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 897 | if (convertAlignment(g, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:131:14: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutputFormat, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score >; TSeqFile = std::__cxx11::basic_string; TMethod = unsigned int; TDiag = int; TOutputFormat = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | write(strmWrite, gAlign, sequenceNames, FastaFormat()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:215:76: required from ‘void _initAlignParams(const Options&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 215 | pairwise_align >(sc, seqfile, method, low, high, banded, options.outputFormat, outfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align/pair_align.cpp:316:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 316 | _initAlignParams(options, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >; TValue = String >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = String >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = String >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = String >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = String >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = String >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = String >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::HtmlToolDocPrinter_::_toHtml(const TSequence&) const [with TSequence = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/tool_doc.h:284:34: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘TSequence seqan::HtmlToolDocPrinter_::_toHtml(const TSequence&) const [with TSequence = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 11%] Linking CXX executable ../../../bin/pair_align cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/pair_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/pair_align.dir/pair_align.cpp.o -o ../../../bin/pair_align -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 11%] Built target pair_align make -f core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 12%] Building CXX object core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -MF CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o.d -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/prepare_sam.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/prepare_sam.cpp:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/prepare_sam.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:120:16: required from ‘seqan::String >::String(seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 120 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/prepare_sam.cpp:80:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 80 | Dna5String seqFirstRC = seqFirst; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 12%] Linking CXX executable ../../../bin/rabema_prepare_sam cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../../bin/rabema_prepare_sam -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 12%] Built target rabema_prepare_sam make -f core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 12%] Building CXX object core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:42: /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:105:10: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:88:7: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 88 | class ModifiedIterator /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:254:100: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:507:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 507 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:257:91: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = const Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:218:55: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 218 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:336:62: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 336 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:591:16: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 591 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:723:19: required from ‘void seqan::setHost(Pattern >&, const TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 723 | _patternFirstInit(pattern, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:497:10: required from ‘seqan::Pattern >::Pattern(const TNeedle2&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 497 | setHost(*this, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/find_myers_ukkonen_reads.h:108:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 108 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:411:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 411 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:901:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, TStreamOrReader&, seqan::BamIOContext > > >&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&, const TFormat&) [with TPatternSpec = seqan::Tag; TStreamOrReader = seqan::RecordReader, seqan::SinglePass >; TFormat = seqan::Tag; TErrorCurves = std::map >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 901 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 902 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:1252:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1252 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, samReader, bamIOContext, readNameStore, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | refNameStore, faiIndex, options, MyersUkkonenReads(), Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:624:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 624 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:624:9: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 624 | return ModifiedString(host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:218:55: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 218 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:336:62: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 336 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:591:16: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 591 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:723:19: required from ‘void seqan::setHost(Pattern >&, const TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 723 | _patternFirstInit(pattern, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:497:10: required from ‘seqan::Pattern >::Pattern(const TNeedle2&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 497 | setHost(*this, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/find_myers_ukkonen_reads.h:108:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 108 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:411:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 411 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:901:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, TStreamOrReader&, seqan::BamIOContext > > >&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&, const TFormat&) [with TPatternSpec = seqan::Tag; TStreamOrReader = seqan::RecordReader, seqan::SinglePass >; TFormat = seqan::Tag; TErrorCurves = std::map >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 901 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 902 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:1252:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1252 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, samReader, bamIOContext, readNameStore, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | refNameStore, faiIndex, options, MyersUkkonenReads(), Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:426:11: required from ‘int seqan::readRegion(String&, const FaiIndex&, unsigned int, unsigned int, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 426 | resize(str, toRead, TValue()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:505:22: required from ‘int seqan::readSequence(String&, const FaiIndex&, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 505 | return readRegion(str, index, refId, 0, sequenceLength(index, refId)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:869:29: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, TStreamOrReader&, seqan::BamIOContext > > >&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&, const TFormat&) [with TPatternSpec = seqan::Tag; TStreamOrReader = seqan::RecordReader, seqan::SinglePass >; TFormat = seqan::Tag; TErrorCurves = std::map >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 869 | if (readSequence(contig, faiIndex, faiRefId) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_build_gold_standard.cpp:1252:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1252 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, samReader, bamIOContext, readNameStore, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | refNameStore, faiIndex, options, MyersUkkonenReads(), Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 14%] Linking CXX executable ../../../bin/rabema_build_gold_standard cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../../bin/rabema_build_gold_standard -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 14%] Built target rabema_build_gold_standard make -f core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make core/apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 16%] Building CXX object core/apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:28: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1886:15: required from ‘void seqan::findIntervals(const IntervalTree&, TValue, String&) [with TValue = unsigned int; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1886 | findIntervals(it.g,it.pm,query,result); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:635:22: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamIOContext > > >&, const seqan::String&, const seqan::StringSet > >&, const seqan::NameStoreCache > > >&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 635 | findIntervals(intervalTrees[seqId], lastPos, queryResult); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:976:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, TStreamOrReader&, seqan::BamIOContext > > >&, const seqan::StringSet > >&, const seqan::NameStoreCache > > >&, const seqan::StringSet, seqan::Alloc<> > >&, seqan::RecordReader&, const RabemaEvaluationOptions&, const TPatternSpec&, const TFormat&) [with TStreamOrReader = seqan::RecordReader, seqan::SinglePass >; TGsiStream = seqan::Stream >; TGsiStreamSpec = seqan::SinglePass; TPatternSpec = seqan::Tag; TFormat = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 976 | int res = benchmarkReadResult(result, currentSamRecords, bamIOContext, currentGsiRecords, refNameStore, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 977 | refNameStoreCache, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 978 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:1402:49: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1402 | res = compareAlignedReadsToReference(result, samReader, bamIOContext, refNameStore, refNameStoreCache, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1403 | refSeqs, gsiReader, options, MyersUkkonenReads(), Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1827:26: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1827 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1838:43: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1838 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1859:51: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1859 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:1311:16: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1311 | reserve(refSeqs[i], sequenceLength(faiIndex, i), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = const Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:218:55: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:336:62: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 336 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:591:16: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 591 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:723:19: required from ‘void seqan::setHost(Pattern >&, const TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 723 | _patternFirstInit(pattern, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:497:10: required from ‘seqan::Pattern >::Pattern(const TNeedle2&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 497 | setHost(*this, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/find_myers_ukkonen_reads.h:108:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:611:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamIOContext > > >&, const seqan::String&, const seqan::StringSet > >&, const seqan::NameStoreCache > > >&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 611 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:976:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, TStreamOrReader&, seqan::BamIOContext > > >&, const seqan::StringSet > >&, const seqan::NameStoreCache > > >&, const seqan::StringSet, seqan::Alloc<> > >&, seqan::RecordReader&, const RabemaEvaluationOptions&, const TPatternSpec&, const TFormat&) [with TStreamOrReader = seqan::RecordReader, seqan::SinglePass >; TGsiStream = seqan::Stream >; TGsiStreamSpec = seqan::SinglePass; TPatternSpec = seqan::Tag; TFormat = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 976 | int res = benchmarkReadResult(result, currentSamRecords, bamIOContext, currentGsiRecords, refNameStore, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 977 | refNameStoreCache, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 978 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:1402:49: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1402 | res = compareAlignedReadsToReference(result, samReader, bamIOContext, refNameStore, refNameStoreCache, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1403 | refSeqs, gsiReader, options, MyersUkkonenReads(), Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:624:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 624 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:624:9: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 624 | return ModifiedString(host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:218:55: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 218 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:336:62: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 336 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:591:16: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 591 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:723:19: required from ‘void seqan::setHost(Pattern >&, const TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 723 | _patternFirstInit(pattern, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:497:10: required from ‘seqan::Pattern >::Pattern(const TNeedle2&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 497 | setHost(*this, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/find_myers_ukkonen_reads.h:108:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 108 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:611:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamIOContext > > >&, const seqan::String&, const seqan::StringSet > >&, const seqan::NameStoreCache > > >&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 611 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:976:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, TStreamOrReader&, seqan::BamIOContext > > >&, const seqan::StringSet > >&, const seqan::NameStoreCache > > >&, const seqan::StringSet, seqan::Alloc<> > >&, seqan::RecordReader&, const RabemaEvaluationOptions&, const TPatternSpec&, const TFormat&) [with TStreamOrReader = seqan::RecordReader, seqan::SinglePass >; TGsiStream = seqan::Stream >; TGsiStreamSpec = seqan::SinglePass; TPatternSpec = seqan::Tag; TFormat = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 976 | int res = benchmarkReadResult(result, currentSamRecords, bamIOContext, currentGsiRecords, refNameStore, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 977 | refNameStoreCache, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 978 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/rabema_evaluate.cpp:1402:49: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1402 | res = compareAlignedReadsToReference(result, samReader, bamIOContext, refNameStore, refNameStoreCache, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1403 | refSeqs, gsiReader, options, MyersUkkonenReads(), Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 16%] Linking CXX executable ../../../bin/rabema_evaluate cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../../bin/rabema_evaluate -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 16%] Built target rabema_evaluate make -f core/apps/rabema/CMakeFiles/rabema_do_search.dir/build.make core/apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/rabema/CMakeFiles/rabema_do_search.dir/build.make core/apps/rabema/CMakeFiles/rabema_do_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 16%] Building CXX object core/apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o -MF CMakeFiles/rabema_do_search.dir/do_search.cpp.o.d -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:3: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:11: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:13: /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:105:10: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:7: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:88:7: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 88 | class ModifiedIterator /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:254:100: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:507:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 507 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/curve_smoothing.h:257:91: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:23:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 23 | Dna5String contig = argv[1]; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = const Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:218:55: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:336:62: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 336 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:591:16: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 591 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:723:19: required from ‘void seqan::setHost(Pattern >&, const TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 723 | _patternFirstInit(pattern, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:497:10: required from ‘seqan::Pattern >::Pattern(const TNeedle2&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 497 | setHost(*this, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/find_myers_ukkonen_reads.h:108:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:624:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 624 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:624:9: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 624 | return ModifiedString(host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:218:55: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 218 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_begin.h:336:62: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 336 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:591:16: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 591 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:723:19: required from ‘void seqan::setHost(Pattern >&, const TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 723 | _patternFirstInit(pattern, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:497:10: required from ‘seqan::Pattern >::Pattern(const TNeedle2&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 497 | setHost(*this, ndl); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/find_myers_ukkonen_reads.h:108:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 108 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 16%] Linking CXX executable ../../../bin/rabema_do_search cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../../bin/rabema_do_search -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 16%] Built target rabema_do_search make -f core/apps/razers/CMakeFiles/razers.dir/build.make core/apps/razers/CMakeFiles/razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/razers /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/razers/CMakeFiles/razers.dir/build.make core/apps/razers/CMakeFiles/razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 17%] Building CXX object core/apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/razers/CMakeFiles/razers.dir/razers.cpp.o -MF CMakeFiles/razers.dir/razers.cpp.o.d -o CMakeFiles/razers.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:28, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:50: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:715:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 715 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:747:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 747 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:779:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 779 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/outputFormat.h:30, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/outputFormat.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:55: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:237:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp: In function ‘seqan::ArgumentParser::ParseResult extractOptions(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions<>&, seqan::ParamChooserOptions&, seqan::CharString&, const seqan::ArgumentParser&)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:548:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 548 | else if (endsWith(tmp, ".gff")) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:551:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 551 | if (isSet(parser, "shape")) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:585:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 585 | if ((getArgumentValueCount(parser, 1) == 0) && (stop = true)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 587 | if ((options.minClippedLen < 0) && (stop = true)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:508:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: 508 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~~~~^ 509 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:587:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1490:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1490 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1736:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1736 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1490:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1490 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:13: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:410:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 410 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:211:9: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 211 | reserve(reads.concat, length(reads.concat), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:178:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 178 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:410:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 410 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:162: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1718:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1718 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:76: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1718:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1718 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1490:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1490 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:508:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 508 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^ 509 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1491:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1491 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:508:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 508 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^ 509 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2306:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2306 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1718:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1718 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2306:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2306 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2309:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2309 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1718:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1718 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2309:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2309 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1823:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1823 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:391:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 391 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1685:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1685 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:56, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:391:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 391 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1685:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1685 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:391:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 391 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1685:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1685 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1712:17: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1712 | indexRequire(host(swiftPattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2068:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2068 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2233:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2233 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String >; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1474:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1474 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:508:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 508 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^ 509 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1492:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1492 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:508:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 508 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^ 509 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1128:31: required from ‘static void seqan::AssignString_::assign_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1128 | arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1176:42: required from ‘void seqan::assign(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1176 | AssignString_ >::assign_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1108:11: required from ‘void seqan::assign(String&, const TSource&) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1108 | assign(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:173:15: required from ‘seqan::String >& seqan::String >::operator=(const TSource&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 173 | assign(*this, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/outputFormat.h:918:13: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 918 | gInf = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:241:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 241 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:199:14: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 199 | appendValue(reads, seq[0], Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:178:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 178 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:18: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 793 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:1497:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1497 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:508:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 508 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^ 509 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2303 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:199:14: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 199 | appendValue(reads, seq[0], Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:178:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 178 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:484:9: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 484 | resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:679:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 679 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2295:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2295 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:444:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 444 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2298:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2298 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:679:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 679 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 153 | assignValue(*this, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:267:4: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:410:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 410 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers_matepairs.h:797:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 797 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2230:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2230 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.h:2292:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2292 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:218:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:699:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 699 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:679:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 679 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /usr/include/c++/14/string:51: In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11, inlined from ‘void seqan::_parse_readShape(TFile&, TChar&, CharString&) [with TFile = std::basic_fstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:861:15, inlined from ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::basic_fstream; TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:1068:25, inlined from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:1342:26: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/razers.cpp:52: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h: In function ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/paramChooser.h:1043:10: note: ‘c’ declared here 1043 | char c = _streamGet(file); | ^ [ 17%] Building CXX object core/apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -MF CMakeFiles/razers.dir/param_tabs.cpp.o.d -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/razers/param_tabs.cpp [ 19%] Linking CXX executable ../../../bin/razers cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../../bin/razers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 19%] Built target razers make -f core/apps/razers2/CMakeFiles/razers2.dir/build.make core/apps/razers2/CMakeFiles/razers2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2 /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2/CMakeFiles/razers2.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/razers2/CMakeFiles/razers2.dir/build.make core/apps/razers2/CMakeFiles/razers2.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 19%] Building CXX object core/apps/razers2/CMakeFiles/razers2.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2 && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/razers2/CMakeFiles/razers2.dir/razers.cpp.o -MF CMakeFiles/razers2.dir/razers.cpp.o.d -o CMakeFiles/razers2.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:28, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:488:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 488 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:535:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:583:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 583 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:630:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 630 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:127:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 127 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:169:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 169 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:51: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:228:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 228 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp: In function ‘seqan::ArgumentParser::ParseResult extractOptions(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions<>&, seqan::ParamChooserOptions&, seqan::CharString&, const seqan::ArgumentParser&)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:492:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 492 | if (!isSet(parser, "read-naming") && options.outputFormat == 4) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:495:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 495 | if (isSet(parser, "shape")) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:529:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 529 | if ((getArgumentValueCount(parser, 1) == 0) && (stop = true)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 532 | options.errorRate = (100.0 - options.errorRate) / 100.0; | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1097:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: 1097 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:532:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1000:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1000 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:57: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1068 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1128:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1128 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, Myers > >, Pattern >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1203:15: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1203 | matchVerify(verifier, infix(swiftFinder), verifier.m.readId, readSet, TSwiftSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1000:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1000 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:57: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1068 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1128:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1128 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1518:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1518 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1000:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1000 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:57: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1068 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1128:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1128 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, Myers > >, Pattern >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1203:15: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1203 | matchVerify(verifier, infix(swiftFinder), verifier.m.readId, readSet, TSwiftSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1518:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1518 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1000:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1000 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:57: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1068 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1128:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1128 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1521:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1521 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1000:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1000 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:57: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1068 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1128:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1128 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, Myers > >, Pattern >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1203:15: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1203 | matchVerify(verifier, infix(swiftFinder), verifier.m.readId, readSet, TSwiftSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1521:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1521 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1000:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1000 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:57: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1068 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1128:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1128 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1097:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1097 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:972:32: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 972 | TSeqIter seqItEnd = end(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1097:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1097 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:13: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:460:16: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 460 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Triple, void>, AlignQualityStoreElement, void>; TSource = Triple, void>, AlignQualityStoreElement, void>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_dequeue.h:344:8: required from ‘void seqan::pushBack(Dequeue&, const TValue&) [with TValue = Triple, void>, AlignQualityStoreElement, void>; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 344 | assign(*me.data_back, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:510:14: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 510 | pushBack(fifo, fL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Triple, void>, seqan::AlignQualityStoreElement, void>& seqan::Triple, void>, seqan::AlignQualityStoreElement, void>::operator=(const seqan::Triple, void>, seqan::AlignQualityStoreElement, void>&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:57, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: because ‘seqan::Triple, void>, seqan::AlignQualityStoreElement, void>’ has user-provided ‘seqan::Triple::Triple(const seqan::Triple&) [with T1 = long int; T2 = seqan::AlignedReadStoreElement, void>; T3 = seqan::AlignQualityStoreElement; TSpec = void]’ 162 | inline Triple(Triple const & _p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:201:9: required from ‘bool seqan::loadReads(FragmentStore&, const char*, const char*, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | reserve(store.readSeqStore.concat, length(store.readSeqStore.concat), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:167:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 167 | if (!loadReads(store, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:460:16: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 460 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:162: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:76: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1049:21: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1049 | TReadPrefixRev readRev(prefix(readSet[readId], ndlLength)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1068:22: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1068 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1518:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1518 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1518:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1518 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1521:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1521 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1521:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1521 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1189 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_anchor.h:465:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 465 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:628:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = String >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 628 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2582:18: required from ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = void; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = False]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2582 | insertGap(gaps, insPos - rBegin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1053:48: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1053 | convertMatchesToGlobalAlignment(store, scoreType, False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:90: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1823:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1823 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:75: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:434:32: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 434 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1190:32: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1190 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:434:32: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 434 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1190:32: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1190 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:434:32: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 434 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1190:32: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1190 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1015:13: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1015 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1069:22: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1069 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = std::basic_ofstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/outputFormat.h:1092:9: required from ‘void seqan::dumpMatches(FragmentStore&, StringSet > >&, String&, CharString, CharString, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1092 | write(file, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:220:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 220 | dumpMatches(store, genomeFileNames, gnoToFileMap, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:481:11: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 481 | assignSeq(firstRead, multiFasta[0], format); // read the first sequence /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:18: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 793 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1073:16: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, TReadSet&, SwiftSemiGlobal) [with TMatchVerifier = MatchVerifier, RazerSOptions<>, String >, InfixSegment>, Myers >, Alloc<> >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > > >; TGenome = String, Alloc<> >; TReadSet = StringSet >, InfixSegment>, Owner<> >; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1073 | while (find(myersFinderRev, myersPatternRev, /*score*/maxScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:542:22: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 542 | if (matchVerify(verifierL, infix(genome, (TSignedGPos)(*it).i2.beginPos, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | matePairId, readSetL, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1515:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1515 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1657:13: required from ‘typename seqan::Size::TMatePairStore>::Type seqan::appendMatePair(FragmentStore&, const TRead&, const TRead&, const CharString&, const CharString&) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TMatePairStore>::Type = long unsigned int; typename FragmentStore::TMatePairStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1657 | appendValue(me.readSeqStore, read1, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:194:17: required from ‘bool seqan::loadReads(FragmentStore&, const char*, const char*, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 194 | appendMatePair(store, seq[0], seq[1], id[0], id[1]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:167:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 167 | if (!loadReads(store, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:484:9: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 484 | resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:617:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 617 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1657:13: required from ‘typename seqan::Size::TMatePairStore>::Type seqan::appendMatePair(FragmentStore&, const TRead&, const TRead&, const CharString&, const CharString&) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TMatePairStore>::Type = long unsigned int; typename FragmentStore::TMatePairStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1657 | appendValue(me.readSeqStore, read1, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:194:17: required from ‘bool seqan::loadReads(FragmentStore&, const char*, const char*, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | appendMatePair(store, seq[0], seq[1], id[0], id[1]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:167:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 167 | if (!loadReads(store, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1507:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1507 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:477:13: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 477 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1199:13: required from ‘void seqan::mapSingleReads(TFragmentStore&, TGenome&, unsigned int, Pattern >&, TPreprocessing&, char, TRazerSOptions&) [with TFragmentStore = FragmentStore<>; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, Myers > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1199 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1321:19: required from ‘int seqan::mapSingleReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1321 | mapSingleReads(store, genome, gseqNo, swiftPattern, forwardPatterns, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1459:24: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1459 | return mapSingleReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1510:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1510 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 22; unsigned int BITSIZE2 = 10]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:617:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 617 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:605:23: required from ‘void seqan::_arrayConstructCopyDefault(TSource1, TSource2, TTarget) [with TTarget = Segment >, InfixSegment>*; TSource1 = Segment >, InfixSegment>*; TSource2 = Segment >, InfixSegment>*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 605 | valueConstruct(target_begin, getValue(source_begin)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1420:31: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, False) [with TValueSource = Segment >, InfixSegment>; TValueTarget = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1420 | _arrayConstructCopyDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = Segment >, InfixSegment>; TValueTarget = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Segment >, InfixSegment>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:1435:18: required from ‘typename seqan::Size >::Type seqan::resize(StringSet&, TSize, Tag) [with TString = Segment >, InfixSegment>; TSpec = Owner<>; TSize = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1435 | return resize(me.strings, new_size, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:731:8: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 731 | resize(readSetL, pairCount, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 153 | assignValue(*this, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:267:4: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:460:16: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 460 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:617:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 617 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Triple, void>, AlignQualityStoreElement, void>; TSource = Triple, void>, AlignQualityStoreElement, void>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:268:11: required from ‘void seqan::move(TTarget&, TSource&) [with TTarget = Triple, void>, AlignQualityStoreElement, void>; TSource = Triple, void>, AlignQualityStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 268 | assign(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1056:13: required from ‘void seqan::_arrayMoveForwardDefault(TSource1, TSource2, TTarget) [with TTarget = Triple, void>, AlignQualityStoreElement, void>*; TSource1 = Triple, void>, AlignQualityStoreElement, void>*; TSource2 = Triple, void>, AlignQualityStoreElement, void>*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1056 | move(*target_begin, *source_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1600:29: required from ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, False) [with TValue = Triple, void>, AlignQualityStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1600 | _arrayMoveForwardDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = Triple, void>, AlignQualityStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1211:25: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = Triple, void>, AlignQualityStoreElement, void>*; TSource1 = Triple, void>, AlignQualityStoreElement, void>*; TSource2 = Triple, void>, AlignQualityStoreElement, void>*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1211 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1295:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:510:14: required from ‘void seqan::mapMatePairReads(FragmentStore&, TGenome&, unsigned int, Pattern >&, Pattern >&, TPreprocessing&, TPreprocessing&, char, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGenome = String, Alloc<> >; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TPreprocessing = String >, InfixSegment>, Myers >, Alloc<> >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 510 | pushBack(fifo, fL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers_matepairs.h:831:21: required from ‘int seqan::mapMatePairReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 831 | mapMatePairReads(store, genome, contigId, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1456:26: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&, const TShape&, Swift) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1456 | return mapMatePairReads(store, genomeFileNameList, gnoToFileMap, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.h:1504:19: required from ‘int seqan::mapReads(FragmentStore&, StringSet > >&, String&, RazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TGNoToFile = Pair >, unsigned int>; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1504 | return mapReads(store, genomeFileNameList, gnoToFileMap, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:201:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 201 | int error = mapReads(store, genomeFileNames, gnoToFileMap, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:633:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Triple, void>, seqan::AlignQualityStoreElement, void>& seqan::Triple, void>, seqan::AlignQualityStoreElement, void>::operator=(const seqan::Triple, void>, seqan::AlignQualityStoreElement, void>&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: because ‘seqan::Triple, void>, seqan::AlignQualityStoreElement, void>’ has user-provided ‘seqan::Triple::Triple(const seqan::Triple&) [with T1 = long int; T2 = seqan::AlignedReadStoreElement, void>; T3 = seqan::AlignQualityStoreElement; TSpec = void]’ 162 | inline Triple(Triple const & _p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51: In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AssignString_::assign_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1128:31, inlined from ‘void seqan::assign(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1176:42, inlined from ‘void seqan::assign(String&, TSource&) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1099:11, inlined from ‘seqan::String >::String(TSource&) [with TSource = char; TValue = char; TSpec = void]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:100:19, inlined from ‘seqan::String > seqan::_parseReadFilepath(TFile&, TChar&) [with TFile = std::basic_ifstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_parsing.h:330:15, inlined from ‘int getGenomeFileNameList(seqan::CharString, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:90:50: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp: In function ‘int getGenomeFileNameList(seqan::CharString, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:73:14: note: ‘c’ declared here 73 | char c = _streamGet(file); | ^ In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11, inlined from ‘seqan::String > seqan::_parseReadFilepath(TFile&, TChar&) [with TFile = std::basic_ifstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_parsing.h:338:9, inlined from ‘int getGenomeFileNameList(seqan::CharString, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:90:50: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp: In function ‘int getGenomeFileNameList(seqan::CharString, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:73:14: note: ‘c’ declared here 73 | char c = _streamGet(file); | ^ In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11, inlined from ‘void seqan::_parse_readShape(TFile&, TChar&, CharString&) [with TFile = std::basic_fstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:861:15, inlined from ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::basic_fstream; TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:1068:25, inlined from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:1342:26: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/razers.cpp:46: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h: In function ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/paramChooser.h:1043:10: note: ‘c’ declared here 1043 | char c = _streamGet(file); | ^ [ 19%] Building CXX object core/apps/razers2/CMakeFiles/razers2.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2 && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/razers2/CMakeFiles/razers2.dir/param_tabs.cpp.o -MF CMakeFiles/razers2.dir/param_tabs.cpp.o.d -o CMakeFiles/razers2.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2/param_tabs.cpp [ 20%] Linking CXX executable ../../../bin/razers2 cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers2.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/razers2.dir/razers.cpp.o CMakeFiles/razers2.dir/param_tabs.cpp.o -o ../../../bin/razers2 -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 20%] Built target razers2 make -f core/apps/sak/CMakeFiles/sak.dir/build.make core/apps/sak/CMakeFiles/sak.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/sak/CMakeFiles/sak.dir/build.make core/apps/sak/CMakeFiles/sak.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 22%] Building CXX object core/apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/sak/CMakeFiles/sak.dir/sak.cpp.o -MF CMakeFiles/sak.dir/sak.cpp.o.d -o CMakeFiles/sak.dir/sak.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:42: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:379:64: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment, Alloc<> >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 379 | for (typename Iterator::Type it = begin(seq, Rooted()); !atEnd(it); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:501:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 501 | if (writeRecord(*outPtr, id, infix(seqCopy, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:379:64: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 379 | for (typename Iterator::Type it = begin(seq, Rooted()); !atEnd(it); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:523:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 523 | if (writeRecord(*outPtr, id, infix(seq, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 524 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 525 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:379:74: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment, Alloc<> >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 379 | for (typename Iterator::Type it = begin(seq, Rooted()); !atEnd(it); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:501:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 501 | if (writeRecord(*outPtr, id, infix(seqCopy, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:379:74: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 379 | for (typename Iterator::Type it = begin(seq, Rooted()); !atEnd(it); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:523:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 523 | if (writeRecord(*outPtr, id, infix(seq, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 524 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 525 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:361:63: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment, Alloc<> >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 361 | typename Iterator::Type it_end = end(seq); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:501:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 501 | if (writeRecord(*outPtr, id, infix(seqCopy, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:361:63: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 361 | typename Iterator::Type it_end = end(seq); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:523:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 523 | if (writeRecord(*outPtr, id, infix(seq, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 524 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 525 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:379:74: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment, Alloc<> >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 379 | for (typename Iterator::Type it = begin(seq, Rooted()); !atEnd(it); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:501:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 501 | if (writeRecord(*outPtr, id, infix(seqCopy, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/write_fasta_fastq.h:379:74: required from ‘int seqan::writeRecord(TStream&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TStream = std::basic_ostream; TIdString = String >; TQualString = Segment >, InfixSegment>; TSeqString = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 379 | for (typename Iterator::Type it = begin(seq, Rooted()); !atEnd(it); ++it) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:523:36: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 523 | if (writeRecord(*outPtr, id, infix(seq, infixBegin, infixEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 524 | infix(quals, infixBegin, infixEnd), seqan::Fastq(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 525 | options.seqOutOptions) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sak/sak.cpp:492:45: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 492 | seqan::Dna5String seqCopy = seq; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 22%] Linking CXX executable ../../../bin/sak cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak && /usr/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sak.dir/sak.cpp.o -o ../../../bin/sak -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 22%] Built target sak make -f core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sam2matrix /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 24%] Building CXX object core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sam2matrix && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -MF CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o.d -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix/sam2matrix.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix/sam2matrix.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix/sam2matrix.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix/sam2matrix.cpp:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:501:40: required from ‘int seqan::SequenceStreamImpl_::readRecord(TId&, TSequence&, const TFormatTag&) [with TId = seqan::String >; TSequence = seqan::String, seqan::Alloc<> >; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 501 | res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:697:38: required from ‘int seqan::readRecord(TId&, TSequence&, SequenceStream&) [with TId = String >; TSequence = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 697 | res = seqIO._impl->readRecord(id, seq, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix/sam2matrix.cpp:155:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 155 | if (readRecord(id, seq, seqStream) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64, from /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix/sam2matrix.cpp:46: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/new_allocator.h:34, from /usr/include/c++/14/ppc64le-redhat-linux/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/stl_tree.h:64: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 24%] Linking CXX executable ../../../bin/sam2matrix cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sam2matrix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../../bin/sam2matrix -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 24%] Built target sam2matrix make -f core/apps/samcat/CMakeFiles/samcat.dir/build.make core/apps/samcat/CMakeFiles/samcat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/samcat /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/samcat /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/samcat/CMakeFiles/samcat.dir/build.make core/apps/samcat/CMakeFiles/samcat.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 25%] Building CXX object core/apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/samcat && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -MF CMakeFiles/samcat.dir/samcat.cpp.o.d -o CMakeFiles/samcat.dir/samcat.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/samcat/samcat.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/samcat/samcat.cpp:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/apps/samcat/samcat.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 25%] Linking CXX executable ../../../bin/samcat cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/samcat && /usr/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/samcat.dir/samcat.cpp.o -o ../../../bin/samcat -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 25%] Built target samcat make -f core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqan_tcoffee /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 25%] Building CXX object core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqan_tcoffee && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:37, from /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:22: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:18: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:39: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:25: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(const Graph&, const TPropertyMap&, TValue, String&) [with TSpec = Directed >; TPropertyMap = String > > > >; TValue = long unsigned int; TCargo = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:576:34: required from ‘void seqan::matchRefinement(TAlignmentString&, StringSet&, TScore&, TOutGraph&, typename Size::Type>::Type, TAnnotation&, Tag) [with TAlignmentString = String >; TAnnotation = bool; TOutGraph = Graph, Alloc<> >, Dependent > >, long unsigned int, Tag > >; TSequence = String, Alloc<> >; TSetSpec = Dependent >; TScore = long unsigned int; TTagSpec = TagExactRefinement_; typename Size::Type>::Type = long unsigned int; typename Value::Type = Fragment<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 576 | findIntervalsExcludeTouching(gs[seq_i_pos],pms[seq_i_pos],node_i,relevant_segments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:700:17: required from ‘void seqan::matchRefinement(TFragmentString&, StringSet&, TOutGraph&) [with TFragmentString = String >; TOutGraph = Graph, Alloc<> >, Dependent > >, long unsigned int, Tag > >; TSequence = String, Alloc<> >; TSetSpec = Dependent >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 700 | matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:229:17: required from ‘void seqan::buildAlignmentGraph(String&, Graph >&, FrequencyCounting) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; FrequencyCounting = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 229 | matchRefinement(matches,strSet,outGraph); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_msa.h:115:21: required from ‘void seqan::evaluateAlignment(const MsaOptions&) [with TAlphabet = SimpleType; TScore = Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 115 | buildAlignmentGraph(matches, g, FrequencyCounting() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:258:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 258 | evaluateAlignment(msaOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:282:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 282 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:2068:26: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 2068 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:2079:43: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 2079 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:2100:51: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 2100 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:21: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:1892:17: required from ‘bool seqan::convertAlignment(const Graph >&, TMatrix&) [with TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; TMatrix = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1892 | TStringSetStr str = label(g,it->second); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_msa.h:145:22: required from ‘void seqan::evaluateAlignment(const MsaOptions&) [with TAlphabet = SimpleType; TScore = Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 145 | if (convertAlignment(g, mat)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:258:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 258 | evaluateAlignment(msaOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:282:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 282 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:1892:17: required from ‘bool seqan::convertAlignment(const Graph >&, TMatrix&) [with TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; TMatrix = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1892 | TStringSetStr str = label(g,it->second); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_msa.h:145:22: required from ‘void seqan::evaluateAlignment(const MsaOptions&) [with TAlphabet = SimpleType; TScore = Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 145 | if (convertAlignment(g, mat)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:258:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 258 | evaluateAlignment(msaOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:302:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 302 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_impl_align.h:1892:17: required from ‘bool seqan::convertAlignment(const Graph >&, TMatrix&) [with TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; TMatrix = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1892 | TStringSetStr str = label(g,it->second); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_msa.h:145:22: required from ‘void seqan::evaluateAlignment(const MsaOptions&) [with TAlphabet = SimpleType; TScore = Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 145 | if (convertAlignment(g, mat)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:258:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 258 | evaluateAlignment(msaOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee/seqan_tcoffee.cpp:322:34: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 322 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 25%] Linking CXX executable ../../../bin/seqan_tcoffee cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqan_tcoffee && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../../bin/seqan_tcoffee -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 25%] Built target seqan_tcoffee make -f core/apps/seqcons/CMakeFiles/seqcons.dir/build.make core/apps/seqcons/CMakeFiles/seqcons.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqcons /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqcons/CMakeFiles/seqcons.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/seqcons/CMakeFiles/seqcons.dir/build.make core/apps/seqcons/CMakeFiles/seqcons.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 27%] Building CXX object core/apps/seqcons/CMakeFiles/seqcons.dir/seqcons.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqcons && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/seqcons/CMakeFiles/seqcons.dir/seqcons.cpp.o -MF CMakeFiles/seqcons.dir/seqcons.cpp.o.d -o CMakeFiles/seqcons.dir/seqcons.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:37, from /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:24: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:23: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:42: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h: In function ‘void seqan::getGappedConsensus(FragmentStore&, TGappedConsensus&, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:387:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 387 | for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 389 | diff = (itGaps->gapPos - itGaps->seqPos); | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:91:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:102:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 102 | public ::std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp: In function ‘seqan::ArgumentParser::ParseResult parseCommandLine(seqan::ConsensusOptions&, int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:94:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 94 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:98:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 98 | getOptionValue(consOpt.readsfile, parser, "reads"); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:240:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 240 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 244 | typedef FragmentStore<> TFragmentStore; | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:207:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: 207 | write(strmWrite, fragStore, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:244:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:207:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 207 | write(strmWrite, fragStore, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:972:32: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 972 | TSeqIter seqItEnd = end(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:207:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 207 | write(strmWrite, fragStore, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(const Graph&, const TPropertyMap&, TValue, String&) [with TSpec = Directed >; TPropertyMap = String > > > >; TValue = long unsigned int; TCargo = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:576:34: required from ‘void seqan::matchRefinement(TAlignmentString&, StringSet&, TScore&, TOutGraph&, typename Size::Type>::Type, TAnnotation&, Tag) [with TAlignmentString = String >; TAnnotation = bool; TOutGraph = Graph >, Dependent > >, long unsigned int, Tag > >; TSequence = String >; TSetSpec = Dependent >; TScore = long unsigned int; TTagSpec = TagExactRefinement_; typename Size::Type>::Type = long unsigned int; typename Value::Type = Fragment<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 576 | findIntervalsExcludeTouching(gs[seq_i_pos],pms[seq_i_pos],node_i,relevant_segments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:700:17: required from ‘void seqan::matchRefinement(TFragmentString&, StringSet&, TOutGraph&) [with TFragmentString = String >; TOutGraph = Graph >, Dependent > >, long unsigned int, Tag > >; TSequence = String >; TSetSpec = Dependent >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 700 | matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:182:17: required from ‘void seqan::buildAlignmentGraph(String&, String&, Graph >&, FractionalScore) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TScoreValue = int; TSpec2 = Alloc<>; TStringSet = StringSet >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; FractionalScore = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 182 | matchRefinement(matches,strSet,outGraph); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:311:21: required from ‘void seqan::buildAlignmentGraph(String&, String&, Graph >&, const TScore&, ReScore) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TScoreValue = int; TSpec2 = Alloc<>; TStringSet = StringSet >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; TScore = Score >; ReScore = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 311 | buildAlignmentGraph(matches, scores, outGraph, FractionalScore() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:564:21: required from ‘void seqan::consensusAlignment(Graph >&, String >&, const TConfigOptions&) [with TStringSet = StringSet >, Dependent > >; TCargo = void; TSpec = const Tag; TSize = long unsigned int; TConfigOptions = ConsensusOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 564 | buildAlignmentGraph(matches, scores, g, consOpt.sc, ReScore() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:278:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 278 | consensusAlignment(gOut, begEndPos, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:2068:26: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 2068 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:2079:43: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 2079 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:2100:51: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 2100 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:207:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 207 | write(strmWrite, fragStore, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:90: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:75: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1189 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_anchor.h:465:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 465 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2801:19: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2801 | insertGaps(gaps, insPos - rBegin, blkLen); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:459:45: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 459 | convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:184:7: required from ‘int loadFiles(TFragmentStore&, TSize&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>; TSize = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 184 | read(strmReads, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:250:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 250 | int ret = loadFiles(fragStore, numberOfContigs, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1477:56: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >; TValue = const seqan::SimpleType; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1477 | typename Size::Type new_length = reserve(me, me_length + 1, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TValue = SimpleType; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_realign.h:776:15: required from ‘void seqan::reAlign(FragmentStore&, TScore&, TId, TMethod, TBandwidth, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TScore = Score >, Score > > >; TId = long unsigned int; TMethod = int; TBandwidth = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 776 | appendValue(contigEl.seq, (TAlphabet)value(itConsensus), Generous() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:263:12: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 263 | reAlign(fragStore, combinedScore, currentContig, consOpt.rmethod, consOpt.bandwidth, consOpt.include); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:221:19: required from ‘void seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 221 | op = (*it1 == *it2)? 'M': 'R'; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:475:16: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, TContig&, TReadSeq&, TAlignedRead&, TErrors&, const Nothing&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement >, GapAnchor, void>; TReadSeq = String >; TErrors = int; TAlignedRead = AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1058:35: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; TAlignFunctor = Nothing; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1058 | alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1210:25: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1210 | _writeAlignments(target, store, Sam(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1239:25: required from ‘void seqan::write(TFile&, FragmentStore&, Sam) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1239 | _writeAlignments(target, store, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:220:8: required from ‘int writeOutput(TFragmentStore&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 220 | write(strmWrite, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:308:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 308 | ret = writeOutput(fragStore, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1396:13: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, TId) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; TId = unsigned int; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1396 | appendValue(me.readSeqStore, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:1545:14: required from ‘int seqan::_convertSimpleReadFile(TFile&, FragmentStore&, TFilePath&, bool) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TFilePath = const std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1545 | appendRead(fragStore, seq, fragId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:166:29: required from ‘int loadFiles(TFragmentStore&, TSize&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>; TSize = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 166 | if (_convertSimpleReadFile(strmReads, fragStore, consOpt.readsfile, moveToFront) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:250:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 250 | int ret = loadFiles(fragStore, numberOfContigs, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2738:18: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2738 | TContigGapsPW contigGapsPW(/*contigInfix, */gaps[(*it).id]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:459:45: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 459 | convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:184:7: required from ‘int loadFiles(TFragmentStore&, TSize&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>; TSize = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 184 | read(strmReads, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:250:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 250 | int ret = loadFiles(fragStore, numberOfContigs, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder >, InfixSegment>, Tag >; TValue = Segment >, InfixSegment>; typename Value::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment >, InfixSegment>; TValue2 = const Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment >, InfixSegment>; TSource = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2739:15: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2739 | TReadGaps readGaps(store.readSeqStore[(*it).readId], (*it).gaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:459:45: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 459 | convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:184:7: required from ‘int loadFiles(TFragmentStore&, TSize&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>; TSize = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 184 | read(strmReads, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:250:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 250 | int ret = loadFiles(fragStore, numberOfContigs, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1396:13: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, TId) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; TId = unsigned int; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1396 | appendValue(me.readSeqStore, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:1545:14: required from ‘int seqan::_convertSimpleReadFile(TFile&, FragmentStore&, TFilePath&, bool) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TFilePath = const std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1545 | appendRead(fragStore, seq, fragId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:166:29: required from ‘int loadFiles(TFragmentStore&, TSize&, const seqan::ConsensusOptions&) [with TFragmentStore = seqan::FragmentStore<>; TSize = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 166 | if (_convertSimpleReadFile(strmReads, fragStore, consOpt.readsfile, moveToFront) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons/seqcons.cpp:250:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 250 | int ret = loadFiles(fragStore, numberOfContigs, consOpt); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:56, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorRead(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:534:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 534 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:535:13: note: here 535 | case 'I': | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorRead(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:534:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 534 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:535:13: note: here 535 | case 'I': | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorContig(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:564:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 564 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:565:13: note: here 565 | case 'D': | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘typename seqan::Size::Type seqan::reserve(T&, const TSize&) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2091:19, inlined from ‘void seqan::upgmaTree(Graph >&, Graph >&, TTag) [with TValue = double; TSpec1 = Tag; TCargo = double; TSpec2 = Tag; TTag = Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:854:9, inlined from ‘void seqan::upgmaTree(TDistance&, Graph >&) [with TDistance = Graph >; TCargo = double; TSpec = Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:965:11, inlined from ‘void seqan::consensusAlignment(Graph >&, String >&, const TConfigOptions&) [with TStringSet = StringSet >, Dependent > >; TCargo = void; TSpec = const Tag; TSize = long unsigned int; TConfigOptions = ConsensusOptions]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:570:11: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::consensusAlignment(Graph >&, String >&, const TConfigOptions&) [with TStringSet = StringSet >, Dependent > >; TCargo = void; TSpec = const Tag; TSize = long unsigned int; TConfigOptions = ConsensusOptions]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 27%] Linking CXX executable ../../../bin/seqcons cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqcons && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqcons.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/seqcons.dir/seqcons.cpp.o -o ../../../bin/seqcons -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 27%] Built target seqcons make -f core/apps/snp_store/CMakeFiles/snp_store.dir/build.make core/apps/snp_store/CMakeFiles/snp_store.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/snp_store /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/snp_store/CMakeFiles/snp_store.dir/build.make core/apps/snp_store/CMakeFiles/snp_store.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 27%] Building CXX object core/apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/snp_store && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o -MF CMakeFiles/snp_store.dir/snp_store.cpp.o.d -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:32: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:33: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:34: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:43, from /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h: In function ‘void seqan::getGappedConsensus(FragmentStore&, TGappedConsensus&, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:387:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 387 | for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 389 | diff = (itGaps->gapPos - itGaps->seqPos); | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:91:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:102:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 102 | public ::std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:53: /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:356:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 356 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:405:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 405 | struct LessPosLen : public ::std::binary_function < TPosLen, TPosLen, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:420:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 420 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:468:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 468 | struct LessId : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:481:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 481 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:504:40: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 504 | struct LessGPosEnd : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:523:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 523 | struct LessGPosEndOa : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:545:36: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 545 | struct HigherQ : public ::std::binary_function < TQual, TQual, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_base.h: In instantiation of ‘seqan::Pair::Pair(const T1&, const T2&) [with T1 = unsigned int; T2 = seqan::Segment >, seqan::InfixSegment>; TSpec = void]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:5235:46: required from ‘void seqan::dumpShortIndelPolymorphismsBatch(TFragmentStore&, TReadCigars&, TGenome&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TGenome = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 5235 | Pair(1,rInf))); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:997:74: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 997 | if(!options.realign) dumpShortIndelPolymorphismsBatch(fragmentStore, readCigars, fragmentStore.contigStore[0].seq, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, indelFileStream, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1442:28: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 1442 | int result = detectSNPs(options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_base.h:143:53: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 143 | Pair(T1 const & _i1, T2 const & _i2) : i1(_i1), i2(_i2) {} | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1189 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:4144:36: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCounts = String >; TReadCigars = StringSet > >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 4144 | TContigGapIter refIt = iter(referenceGaps,candidateViewPos-refStart); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:2564:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2564 | dumpVariantsRealignBatch(fragStoreGroup,readCigars, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2565 | readCounts,genomeID, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~ 2566 | groupStartCoord,groupStartPos,groupEndPos, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2567 | fileSNPs,fileIndels,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1012:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1012 | dumpVariantsRealignBatchWrap(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,indelFileStream,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1442:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1442 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1200:28: required from ‘typename seqan::Iterator >::Type seqan::iter(const T&, TPos, Tag) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1200 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1178:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(const T&, TPos) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1178 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_anchor.h:450:22: required from ‘bool seqan::isGap(const Gaps >&, TPosition) [with TSequence = String >; TGapAnchors = String, Alloc<> >; TPosition = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 450 | return isGap(iter(gaps, clippedViewPos)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:4505:72: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCounts = String >; TReadCigars = StringSet > >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 4505 | ((indelConsens[candidateViewPos].i1 & 7) == 6 && isGap(referenceGaps, candidateViewPos-refStart))) // position in consensus is the same as in reference /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:2564:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2564 | dumpVariantsRealignBatch(fragStoreGroup,readCigars, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2565 | readCounts,genomeID, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~ 2566 | groupStartCoord,groupStartPos,groupEndPos, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2567 | fileSNPs,fileIndels,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1012:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1012 | dumpVariantsRealignBatchWrap(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,indelFileStream,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1442:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1442 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/tokenize.h:943:12: required from ‘int seqan::readNChars(TBuffer&, RecordReader&, unsigned int) [with TBuffer = String >; TStream = std::basic_fstream; TPass = SinglePass]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 943 | reserve(buffer, n, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:1004:39: required from ‘int seqan::readMatchesFromGFF_Batch(TFile&, TFragmentStore&, TReadCounts&, String >&, StringSet&, TGenome&, TGenomeIdMap&, TSize, TContigPos, TContigPos, TValue&, TOptions&, bool) [with TFile = std::basic_fstream*; TFragmentStore = FragmentStore; TReadCounts = String >; TCigarStr = String >; TGenome = String >; TGenomeIdMap = std::map >, unsigned int>; TContigPos = long int; TSize = unsigned int; TValue = int; TOptions = SNPCallingOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1004 | if (readNChars(curr_read, reader, 1) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:903:54: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 903 | result = readMatchesFromGFF_Batch(readFileStreams[j], fragmentStore, readCounts, readClips, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 904 | readCigars, genomes[i], gIdStringToIdNumMap, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 905 | i, currentWindowBegin, currentWindowEnd, highestChrId[j], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1442:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1442 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:4809:28: required from ‘void seqan::dumpSNPsBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 4809 | Dna5String gInf = infix(genome, currentBegin, currentEnd); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1014:38: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | dumpSNPsBatch(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.cpp:1442:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1442 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51: In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11, inlined from ‘int seqan::readMatchesFromGFF_Batch(TFile&, TFragmentStore&, TReadCounts&, String >&, StringSet&, TGenome&, TGenomeIdMap&, TSize, TContigPos, TContigPos, TValue&, TOptions&, bool) [with TFile = std::basic_fstream*; TFragmentStore = FragmentStore; TReadCounts = String >; TCigarStr = String >; TGenome = String >; TGenomeIdMap = std::map >, unsigned int>; TContigPos = long int; TSize = unsigned int; TValue = int; TOptions = SNPCallingOptions<>]’ at /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:1082:39: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘’ with type ‘const char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h: In function ‘int seqan::readMatchesFromGFF_Batch(TFile&, TFragmentStore&, TReadCounts&, String >&, StringSet&, TGenome&, TGenomeIdMap&, TSize, TContigPos, TContigPos, TValue&, TOptions&, bool) [with TFile = std::basic_fstream*; TFragmentStore = FragmentStore; TReadCounts = String >; TCigarStr = String >; TGenome = String >; TGenomeIdMap = std::map >, unsigned int>; TContigPos = long int; TSize = unsigned int; TValue = int; TOptions = SNPCallingOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store/snp_store.h:1082:39: note: ‘’ declared here 1082 | append(temp_read,'A'); // will be replaced with correct base in "mutations" loop | ~~~~~~^~~~~~~~~~~~~~~ [ 29%] Linking CXX executable ../../../bin/snp_store cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/snp_store && /usr/bin/cmake -E cmake_link_script CMakeFiles/snp_store.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/snp_store.dir/snp_store.cpp.o -o ../../../bin/snp_store -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 29%] Built target snp_store make -f core/apps/splazers/CMakeFiles/splazers.dir/build.make core/apps/splazers/CMakeFiles/splazers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/splazers /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/splazers/CMakeFiles/splazers.dir/build.make core/apps/splazers/CMakeFiles/splazers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 29%] Building CXX object core/apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/splazers && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o -MF CMakeFiles/splazers.dir/splazers.cpp.o.d -o CMakeFiles/splazers.dir/splazers.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:28, from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:50: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:712:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 712 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:740:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 740 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:766:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 766 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:784:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 784 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:806:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 806 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:51: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:52: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h: In function ‘int seqan::qualityDistributionFromPrbFile(TFile&, TDistribution&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:198:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 198 | if (skipWhitespaces(reader) != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:201:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 201 | int kickout = 0; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h: In function ‘int seqan::qualityDistributionFromFastQIntFile(TFile&, TDistribution&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:373:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 373 | if (pm_options.verbose) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:376:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 376 | resize(avg,pm_options.totalN,(TFloat)0.0); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h: In function ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:934:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 934 | if (value(reader) == 'e') | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:938:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 938 | bool atLeastOneFound = false; | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:59: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:525:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:564:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 564 | for (unsigned i = 0; i < length(readFileNames); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:567:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 567 | if(length(readFileNames) == 2) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:615:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if ((getArgumentValueCount(parser, 1) == 0) && (stop = true)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 617 | if ((options.minClippedLen < 0) && (stop = true)) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment >, seqan::InfixSegment>&; THost = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_shortcuts.h:584:9: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: 584 | return TRevComp(host); /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:1589:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: 1589 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:305:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: 305 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:617:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:161:13: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 161 | _host(std::forward(host)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 165 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:62: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2570:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 2570 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~^~~~ 2571 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2572 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~ 2573 | readSet,//readSetR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~~~~~ 2574 | forwardPatternsR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~~~ 2575 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~ 2576 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~ 2577 | LongestSuffix())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:684:22: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 684 | TGenomeInfix oriInf = inf; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:692:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 692 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestPrefix; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2618:20: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2618 | if (matchVerify( (*it).i2, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~ 2619 | infix(genome, (*it).i2.gBegin, maxEndPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2620 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~ 2621 | readSet, //readSetL /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~ 2622 | forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~ 2623 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~ 2624 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~ 2625 | LongestPrefix()) && /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:684:22: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 684 | TGenomeInfix oriInf = inf; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:692:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 692 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:775:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 775 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^ 776 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 777 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 778 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1466:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1466 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2036:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2036 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2183:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2183 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1466:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1466 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:166:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 166 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:161:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment >, seqan::InfixSegment>&; THost = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 161 | _host(std::forward(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_shortcuts.h:584:9: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 584 | return TRevComp(host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:1589:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1589 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:305:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 305 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:13: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2446:16: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2446 | TSwiftFinderL swiftFinderL(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:13: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:683:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 683 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:516:9: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 516 | reserve(reads.concat, length(reads.concat), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:204:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 204 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2446:16: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2446 | TSwiftFinderL swiftFinderL(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:162: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3068:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3068 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3070:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3070 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:76: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:692:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 692 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2570:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2570 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~ 2571 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2572 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~ 2573 | readSet,//readSetR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~ 2574 | forwardPatternsR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~ 2575 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~ 2576 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~ 2577 | LongestSuffix())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(const Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:537:26: required from ‘void seqan::setHost(ModifiedString&, const THost&) [with THost = Segment >, InfixSegment>; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 537 | me._host = _toPointer(host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:696:10: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 696 | setHost(readRev,infix(readSet[rseqNo],length(readSet[rseqNo])-options.minMatchLen,length(readSet[rseqNo]))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2570:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2570 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~ 2571 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2572 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~ 2573 | readSet,//readSetR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~ 2574 | forwardPatternsR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~ 2575 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~ 2576 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~ 2577 | LongestSuffix())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:477:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 477 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3101:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3101 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3103:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3103 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:683:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 683 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2245 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2248:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2248 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1875:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1875 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1466:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1466 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:775:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 775 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^ 776 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 777 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 778 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2256:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2256 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2259:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2259 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:111:7: required from ‘void seqan::_streamWriteSeq(TTarget&, const TSource&, True) [with TTarget = std::basic_ofstream; TSource = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 111 | class ModifiedIterator > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:219:17: required from ‘void seqan::_streamWrite(TTarget&, const TSource&) [with TTarget = std::basic_ofstream; TSource = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 219 | _streamWriteSeq(target, source, typename IsSequence::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_raw.h:282:14: required from ‘void seqan::write(TFile&, const TData&, const TString&, Raw) [with TFile = std::basic_ofstream; TData = ModifiedString >, InfixSegment>, ModView > > >, Tag >; TString = char [1]; Raw = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 282 | _streamWrite(file, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_raw.h:343:7: required from ‘void seqan::write(TFile&, const TData&) [with TFile = std::basic_ofstream; TData = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 343 | write(file, data, "", Raw()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:807:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = std::basic_ofstream; THost = ModifiedString >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 807 | write(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:1589:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1589 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:305:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 305 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1823:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1823 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:1171:18: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = Finder >, InfixSegment>, Swift > > >; typename Parameter_::Type>::Type = Segment >, InfixSegment>; typename Haystack::Type = const Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1171 | return container(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1628:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const Finder >&) [with THaystack = Segment >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1628 | __int64 textEnd = length(haystack(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1639:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(Finder >&) [with THaystack = Segment >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1639 | return positionRange(const_cast > const &>(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2516:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2516 | gPair = positionRange(swiftFinderL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:801:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 801 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:1171:18: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = Finder >, InfixSegment>, Swift > > >; typename Parameter_::Type>::Type = Segment >, InfixSegment>; typename Haystack::Type = const Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1171 | return container(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1628:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const Finder >&) [with THaystack = Segment >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1628 | __int64 textEnd = length(haystack(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1639:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(Finder >&) [with THaystack = Segment >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1639 | return positionRange(const_cast > const &>(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2516:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2516 | gPair = positionRange(swiftFinderL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:801:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 801 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1823:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1823 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1881:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1881 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2410:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2410 | TReadSetL &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2411:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2411 | TReadSetR &readSetR = host(host(swiftPatternR)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3068:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 3068 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2411:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2411 | TReadSetR &readSetR = host(host(swiftPatternR)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3070:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3070 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:670:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 670 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2570:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2570 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~ 2571 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2572 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~ 2573 | readSet,//readSetR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~ 2574 | forwardPatternsR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~ 2575 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~ 2576 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~ 2577 | LongestSuffix())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:693:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 693 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2570:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2570 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~ 2571 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2572 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~ 2573 | readSet,//readSetR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~ 2574 | forwardPatternsR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~ 2575 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~ 2576 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~ 2577 | LongestSuffix())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:101: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:1735:14: required from ‘bool seqan::combineLeftRight(TMatch&, TMatch&, TRead&, TGenome&, RazerSOptions&, char, SwiftSemiGlobal) [with TMatch = ReadMatch; TRead = const Segment >, InfixSegment>; TGenome = String >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1735 | appendValue(strL,genomeInfL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2728:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2728 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:664:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 664 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:664:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 664 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2245 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:664:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 664 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2248:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2248 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String >; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1450:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1450 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:775:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 775 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^ 776 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 777 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 778 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1468:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1468 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:775:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 775 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^ 776 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 777 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 778 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1128:31: required from ‘static void seqan::AssignString_::assign_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1128 | arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1176:42: required from ‘void seqan::assign(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1176 | AssignString_ >::assign_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1108:11: required from ‘void seqan::assign(String&, const TSource&) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1108 | assign(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:173:15: required from ‘seqan::String >& seqan::String >::operator=(const TSource&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 173 | assign(*this, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:1102:13: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1102 | gInf = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:305:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 305 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:508:14: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 508 | appendValue(reads, seq[0], Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:204:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 204 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:18: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 793 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:704:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 704 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2570:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2570 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~ 2571 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2572 | rseqNo, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~ 2573 | readSet,//readSetR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~ 2574 | forwardPatternsR, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~ 2575 | options, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~ 2576 | TSwiftSpec(), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~ 2577 | LongestSuffix())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1792:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1792 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1912:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1912 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:18: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 793 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:1473:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1473 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:775:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 775 | if (matchVerify( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^ 776 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 777 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 778 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2253 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:670:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 670 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:452:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 452 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:185:61: required from ‘void seqan::_streamWriteSeq(TTarget&, const TSource&, True) [with TTarget = std::basic_ofstream; TSource = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 185 | typename Iterator::Type it = begin(source, Standard()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:219:17: required from ‘void seqan::_streamWrite(TTarget&, const TSource&) [with TTarget = std::basic_ofstream; TSource = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 219 | _streamWriteSeq(target, source, typename IsSequence::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_raw.h:282:14: required from ‘void seqan::write(TFile&, const TData&, const TString&, Raw) [with TFile = std::basic_ofstream; TData = ModifiedString >, InfixSegment>, ModView > > >, Tag >; TString = char [1]; Raw = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 282 | _streamWrite(file, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_raw.h:343:7: required from ‘void seqan::write(TFile&, const TData&) [with TFile = std::basic_ofstream; TData = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 343 | write(file, data, "", Raw()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:807:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = std::basic_ofstream; THost = ModifiedString >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 807 | write(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:1589:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1589 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:305:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 305 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:626:22: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(ModifiedString&, Tag) [with THost = const Segment >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 626 | TResult tmp(begin(host(me), tag_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:497:103: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(const ModifiedString >&, Tag) [with THost = ModifiedString >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 497 | typename Iterator const, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:186:63: required from ‘void seqan::_streamWriteSeq(TTarget&, const TSource&, True) [with TTarget = std::basic_ofstream; TSource = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 186 | typename Iterator::Type it_end = end(source, Standard()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:219:17: required from ‘void seqan::_streamWrite(TTarget&, const TSource&) [with TTarget = std::basic_ofstream; TSource = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 219 | _streamWriteSeq(target, source, typename IsSequence::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_raw.h:282:14: required from ‘void seqan::write(TFile&, const TData&, const TString&, Raw) [with TFile = std::basic_ofstream; TData = ModifiedString >, InfixSegment>, ModView > > >, Tag >; TString = char [1]; Raw = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 282 | _streamWrite(file, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_raw.h:343:7: required from ‘void seqan::write(TFile&, const TData&) [with TFile = std::basic_ofstream; TData = ModifiedString >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 343 | write(file, data, "", Raw()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:807:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = std::basic_ofstream; THost = ModifiedString >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 807 | write(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/outputFormat.h:1589:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1589 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:305:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 305 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:508:14: required from ‘bool seqan::loadReads(TReadSet&, TNameSet&, const char*, const char*, TRazerSOptions&) [with TReadSet = StringSet >, Owner > >; TNameSet = StringSet > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 508 | appendValue(reads, seq[0], Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:204:17: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 204 | if (!loadReads(readSet, readNames, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2728:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2728 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:484:9: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 484 | resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:778:30: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 778 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:702:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 702 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3066:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 3066 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3068:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 3068 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3068:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 3068 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3070:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 3070 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = Segment >, InfixSegment>; TSpec = Owner<>; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, InfixSegment>, Owner<> >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, InfixSegment>, Owner<> >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2481:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2481 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3070:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 3070 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2245 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2245 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2248:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2248 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:717:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 717 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2248:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2248 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:778:30: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 778 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:702:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 702 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 153 | assignValue(*this, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_wotd.h:267:4: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:683:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 683 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_matepairs.h:1046:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1046 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2180:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2180 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2242 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:778:30: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 778 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:702:22: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 702 | if (!chooseParams(options,pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2728:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String >; TOriReadSet = StringSet >, Owner > >; TReadIndexL = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2728 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:2263:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2263 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers_spliced.h:3099:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3099 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/razers.h:2227:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2227 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:274:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers/splazers.cpp:736:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 736 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 29%] Linking CXX executable ../../../bin/splazers cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/splazers && /usr/bin/cmake -E cmake_link_script CMakeFiles/splazers.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/splazers.dir/splazers.cpp.o -o ../../../bin/splazers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 29%] Built target splazers make -f core/apps/stellar/CMakeFiles/stellar.dir/build.make core/apps/stellar/CMakeFiles/stellar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/stellar /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/stellar/CMakeFiles/stellar.dir/build.make core/apps/stellar/CMakeFiles/stellar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 30%] Building CXX object core/apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/stellar && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o -MF CMakeFiles/stellar.dir/stellar.cpp.o.d -o CMakeFiles/stellar.dir/stellar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:24: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:39: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seeds.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:29, from /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:30: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_types.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_types.h:154:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | struct LessPos : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_types.h:206:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct LessLength : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:125:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 125 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 718 | mainWithOptions(options, String()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:58:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 58 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:66:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 66 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:58:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 58 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:66:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 66 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:58:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 58 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:66:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 66 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:58:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 58 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:66:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 66 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:58:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 58 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:66:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 66 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:58:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 58 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:66:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 66 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:89: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:206: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Dependent >; TShape = Shape >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Dependent >; TShape = Shape >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:159:17: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 159 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String >; TSpec1 = Tag; TSource2 = Segment >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:475:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 475 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:101: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String, Alloc<> >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String, Alloc<> >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String, Alloc<> >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String, Alloc<> >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String, Alloc<> >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Dependent > >, IndexQGram, Tag > >; TSource = Index >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String >; TSpec1 = Tag; TSource2 = Segment >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String >; TSize = int; TEps = double; TAlign = seqan::Align >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:703:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:703:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:703:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:703:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:703:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>, InfixSegment>*; TParam = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment >, InfixSegment>, InfixSegment>; typename Value::Type = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment >, InfixSegment>, InfixSegment>; TValue2 = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:703:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:96:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:462:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 462 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:462:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 462 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:462:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 462 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:462:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 462 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:462:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 462 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar_extension.h:402:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:461:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 461 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:462:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 462 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:720:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 720 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:722:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 722 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:724:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 724 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:726:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:466:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 466 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:62:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 62 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:728:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 728 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Triple; TSource = Triple]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:268:11: required from ‘void seqan::move(TTarget&, TSource&) [with TTarget = Triple; TSource = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 268 | assign(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1056:13: required from ‘void seqan::_arrayMoveForwardDefault(TSource1, TSource2, TTarget) [with TTarget = Triple*; TSource1 = Triple*; TSource2 = Triple*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1056 | move(*target_begin, *source_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1600:29: required from ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, False) [with TValue = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1600 | _arrayMoveForwardDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1211:25: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = Triple*; TSource1 = Triple*; TSource2 = Triple*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1211 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1295:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:54:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 54 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:172:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 172 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:688:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 688 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar/stellar.cpp:718:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 718 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘constexpr seqan::Triple& seqan::Triple::operator=(const seqan::Triple&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:57: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: because ‘seqan::Triple’ has user-provided ‘seqan::Triple::Triple(const seqan::Triple&) [with T1 = long unsigned int; T2 = long unsigned int; T3 = int; TSpec = void]’ 162 | inline Triple(Triple const & _p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = ScoreAndID; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = ScoreAndID; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = ScoreAndID; TLess = std::less >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::pop(PriorityType&) [with TValue = ScoreAndID; TLess = std::less >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 30%] Linking CXX executable ../../../bin/stellar cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/stellar && /usr/bin/cmake -E cmake_link_script CMakeFiles/stellar.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/stellar.dir/stellar.cpp.o -o ../../../bin/stellar -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 30%] Built target stellar make -f core/apps/tree_recon/CMakeFiles/tree_recon.dir/build.make core/apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/tree_recon /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f core/apps/tree_recon/CMakeFiles/tree_recon.dir/build.make core/apps/tree_recon/CMakeFiles/tree_recon.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 30%] Building CXX object core/apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/tree_recon && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT core/apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o -MF CMakeFiles/tree_recon.dir/tree_recon.cpp.o.d -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:37, from /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp:19: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp:18: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:39: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp:139:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 139 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp:143:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 143 | typedef double TDistanceValue; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp:165:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 165 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon/tree_recon.cpp:169:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 169 | String names; | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 32%] Linking CXX executable ../../../bin/tree_recon cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/tree_recon && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../../bin/tree_recon -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target tree_recon make -f extras/CMakeFiles/seqan_extras.dir/build.make extras/CMakeFiles/seqan_extras.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/CMakeFiles/seqan_extras.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/CMakeFiles/seqan_extras.dir/build.make extras/CMakeFiles/seqan_extras.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/CMakeFiles/seqan_extras.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target seqan_extras make -f extras/apps/alf/CMakeFiles/alf.dir/build.make extras/apps/alf/CMakeFiles/alf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/alf /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/alf/CMakeFiles/alf.dir/build.make extras/apps/alf/CMakeFiles/alf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Building CXX object extras/apps/alf/CMakeFiles/alf.dir/alf.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/alf && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/alf/CMakeFiles/alf.dir/alf.cpp.o -MF CMakeFiles/alf.dir/alf.cpp.o.d -o CMakeFiles/alf.dir/alf.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:46: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/statistics.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free.h:47, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/statistics.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1980:11: required from ‘seqan::String& seqan::operator+=(String&, const TRight&) [with TLeftValue = SimpleType; TLeftSpec = Alloc<>; TRight = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1980 | append(left, right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/kmer_functions.h:1292:66: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1292 | sequenceCut += infix(sequence, position(itSeq), i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = unsigned int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_base.h:1051:9: required from ‘void seqan::unhash(TString&, THash, unsigned int) [with TString = String, Alloc<> >; THash = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1051 | resize(result, q); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_n2.h:60:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 60 | unhash(w, i, k); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TValue = const seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = String, Alloc<> >; TTargetSpec = Alloc<>; TValue = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = String, Alloc<> >; TString2 = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:181:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 181 | appendValue(mySequenceSet, sequenceTmp, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> > >, IndexQGram > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexQGram >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexQGram >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/statistics/statistics_markov_model.h:303:15: required from ‘void seqan::MarkovModel::build(const seqan::StringSet >&) [with TAlphabet = seqan::SimpleType; TFloat = double; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 303 | indexRequire(ind, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/statistics/statistics_markov_model.h:866:10: required from ‘void seqan::buildMarkovModel(MarkovModel&, StringSet >&) [with TAlphabet = SimpleType; TFloat = double; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 866 | mm.build(stringSet); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/kmer_functions.h:395:21: required from ‘void seqan::countKmers(String >&, MarkovModel&, const TString&, unsigned int) [with TString = String, Alloc<> >; TAlphabetBG = SimpleType; TValue = double]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 395 | buildMarkovModel(backgroundModel, seqSetMM); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_d2z.h:135:23: required from ‘void seqan::_alignmentFreeComparison(Matrix&, const TStringSet&, const AFScore >&) [with TStringSet = StringSet, Alloc<> > >; TValue = double]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 135 | countKmers(*itKmerCounts, *itMM, *itSeqSet, score.kmerSize); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/alignment_free_comparison.h:151:29: required from ‘void seqan::alignmentFreeComparison(Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = StringSet, Alloc<> > >; TValue = double; TComparisonMethod = AFScore >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 151 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:195:32: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 195 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreD2z); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> > >, IndexQGram > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexQGram >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexQGram >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/statistics/statistics_markov_model.h:303:15: required from ‘void seqan::MarkovModel::build(const seqan::StringSet >&) [with TAlphabet = seqan::SimpleType; TFloat = double; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 303 | indexRequire(ind, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/statistics/statistics_markov_model.h:866:10: required from ‘void seqan::buildMarkovModel(MarkovModel&, StringSet >&) [with TAlphabet = SimpleType; TFloat = double; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 866 | mm.build(stringSet); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/kmer_functions.h:395:21: required from ‘void seqan::countKmers(String >&, MarkovModel&, const TString&, unsigned int) [with TString = String, Alloc<> >; TAlphabetBG = SimpleType; TValue = double]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 395 | buildMarkovModel(backgroundModel, seqSetMM); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_d2z.h:135:23: required from ‘void seqan::_alignmentFreeComparison(Matrix&, const TStringSet&, const AFScore >&) [with TStringSet = StringSet, Alloc<> > >; TValue = double]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 135 | countKmers(*itKmerCounts, *itMM, *itSeqSet, score.kmerSize); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/alignment_free_comparison.h:151:29: required from ‘void seqan::alignmentFreeComparison(Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = StringSet, Alloc<> > >; TValue = double; TComparisonMethod = AFScore >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 151 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:195:32: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 195 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreD2z); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1980:11: required from ‘seqan::String& seqan::operator+=(String&, const TRight&) [with TLeftValue = SimpleType; TLeftSpec = Alloc<>; TRight = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1980 | append(left, right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/kmer_functions.h:1292:66: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1292 | sequenceCut += infix(sequence, position(itSeq), i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/kmer_functions.h:850:15: required from ‘void seqan::calculateCovariance(TValue&, const String&, const String&, MarkovModel&, int) [with TValue = double; TSpec = Alloc<>; TAlphabet = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 850 | append(clump, word2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_n2.h:549:48: required from ‘void seqan::_standardiseCounts(TString&, const String >&, const StringSet > >&, const TSequence&, const AFScore >&) [with TString = String; TSequence = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 549 | calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundModel, (len1 + score.kmerSize - 1)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_n2.h:179:27: required from ‘void seqan::_alignmentFreeComparison(Matrix&, const TStringSet&, const AFScore >&) [with TValue = double; TStringSet = StringSet, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 179 | _standardiseCounts(*itStandardisedKmerCounts, revComIndex, kmerNeighbourhood, *itSeqSet, score); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/alignment_free_comparison.h:151:29: required from ‘void seqan::alignmentFreeComparison(Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = StringSet, Alloc<> > >; TValue = double; TComparisonMethod = AFScore >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 151 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:205:32: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 205 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/kmer_functions.h:850:15: required from ‘void seqan::calculateCovariance(TValue&, const String&, const String&, MarkovModel&, int) [with TValue = double; TSpec = Alloc<>; TAlphabet = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 850 | append(clump, word2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_n2.h:549:48: required from ‘void seqan::_standardiseCounts(TString&, const String >&, const StringSet > >&, const TSequence&, const AFScore >&) [with TString = String; TSequence = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 549 | calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundModel, (len1 + score.kmerSize - 1)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/af_n2.h:179:27: required from ‘void seqan::_alignmentFreeComparison(Matrix&, const TStringSet&, const AFScore >&) [with TValue = double; TStringSet = StringSet, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 179 | _standardiseCounts(*itStandardisedKmerCounts, revComIndex, kmerNeighbourhood, *itSeqSet, score); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/alignment_free/alignment_free_comparison.h:151:29: required from ‘void seqan::alignmentFreeComparison(Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = StringSet, Alloc<> > >; TValue = double; TComparisonMethod = AFScore >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 151 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf/alf.cpp:205:32: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 205 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 32%] Linking CXX executable ../../../bin/alf cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/alf && /usr/bin/cmake -E cmake_link_script CMakeFiles/alf.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/alf.dir/alf.cpp.o -o ../../../bin/alf -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target alf make -f extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build.make extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/breakpoint_calculator /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build.make extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Building CXX object extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/breakpoint_calculator.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/breakpoint_calculator && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/breakpoint_calculator.cpp.o -MF CMakeFiles/breakpoint_calculator.dir/breakpoint_calculator.cpp.o.d -o CMakeFiles/breakpoint_calculator.dir/breakpoint_calculator.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator/breakpoint_calculator.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator/breakpoint_calculator.cpp:23: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator/parse_alignment.h:27, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator/breakpoint_calculator.h:34, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator/breakpoint_calculator.cpp:25: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 32%] Linking CXX executable ../../../bin/breakpoint_calculator cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/breakpoint_calculator && /usr/bin/cmake -E cmake_link_script CMakeFiles/breakpoint_calculator.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/breakpoint_calculator.dir/breakpoint_calculator.cpp.o -o ../../../bin/breakpoint_calculator -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target breakpoint_calculator make -f extras/apps/bs_tools/CMakeFiles/bisar.dir/build.make extras/apps/bs_tools/CMakeFiles/bisar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/bs_tools/CMakeFiles/bisar.dir/build.make extras/apps/bs_tools/CMakeFiles/bisar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Building CXX object extras/apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -MF CMakeFiles/bisar.dir/bisar.cpp.o.d -o CMakeFiles/bisar.dir/bisar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:39: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:46: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar_score.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar_score.h:28:57: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 28 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 297 | return value(me); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /usr/include/c++/14/bits/stl_function.h:117:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1289:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 1289 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 294 | postProcessMain(options, BsNonSimple()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:75, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1289:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1289 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1180:37: required from ‘TStream& seqan::operator<<(TStream&, const Gaps&) [with TStream = std::basic_ostream; TSource = String >; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1180 | stream << convert(*it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:127:19: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 127 | std::cout << contigGaps << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1289:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1289 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1180:37: required from ‘TStream& seqan::operator<<(TStream&, const Gaps&) [with TStream = std::basic_ostream; TSource = String >; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1180 | stream << convert(*it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:127:19: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 127 | std::cout << contigGaps << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1289:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1289 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1289:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1289 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1180:37: required from ‘TStream& seqan::operator<<(TStream&, const Gaps&) [with TStream = std::basic_ostream; TSource = String >; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1180 | stream << convert(*it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:127:19: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 127 | std::cout << contigGaps << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1289:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1289 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1256:18: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1256 | TReadSeq readSeq = store.readSeqStore[readId]; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:242:20: required from ‘int writeBsAlignment(TStream&, const seqan::BamIOContext&, TFragmentStore&, TContigGaps&, TId&, TScore&, seqan::BamAlignmentRecord&, TOptions&) [with TStream = std::basic_fstream; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TFragmentStore = seqan::FragmentStore; TContigGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TId = unsigned int; TScore = double; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 242 | Dna5String tmpReadSeq = readSeq; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1194:41: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1194 | writeBsAlignment(outStream, bamIOContext, store, setContigGaps[verifiedMates.alignedReadIdL], verifiedMates.alignedReadIdL, verifiedMates.mapqL, verifiedMates.recordL, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1657:13: required from ‘typename seqan::Size::TMatePairStore>::Type seqan::appendMatePair(FragmentStore&, const TRead&, const TRead&, const CharString&, const CharString&) [with TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TMatePairStore>::Type = long unsigned int; typename FragmentStore::TMatePairStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1657 | appendValue(me.readSeqStore, read1, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar_base.h:102:17: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 102 | appendMatePair(store, seq[0], seq[1], _id[0], _id[1]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1117:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1117 | loadReadsCroppedId(store, options.readFileName, options.readFileName2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1657:13: required from ‘typename seqan::Size::TMatePairStore>::Type seqan::appendMatePair(FragmentStore&, const TRead&, const TRead&, const CharString&, const CharString&) [with TSpec = MyFragmentStoreConfig; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TMatePairStore>::Type = long unsigned int; typename FragmentStore::TMatePairStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1657 | appendValue(me.readSeqStore, read1, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar_base.h:102:17: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 102 | appendMatePair(store, seq[0], seq[1], _id[0], _id[1]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.h:1117:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1117 | loadReadsCroppedId(store, options.readFileName, options.readFileName2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 33%] Linking CXX executable ../../../bin/bisar cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/bisar.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/bisar.dir/bisar.cpp.o -o ../../../bin/bisar -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 33%] Built target bisar make -f extras/apps/bs_tools/CMakeFiles/casbar.dir/build.make extras/apps/bs_tools/CMakeFiles/casbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/bs_tools/CMakeFiles/casbar.dir/build.make extras/apps/bs_tools/CMakeFiles/casbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 35%] Building CXX object extras/apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o -MF CMakeFiles/casbar.dir/casbar.cpp.o.d -o CMakeFiles/casbar.dir/casbar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:42: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h: In function ‘void seqan::getGappedConsensus(FragmentStore&, TGappedConsensus&, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:387:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 387 | for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 389 | diff = (itGaps->gapPos - itGaps->seqPos); | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:91:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:102:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 102 | public ::std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/../../extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:64: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:6, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:72: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:42:57: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:17:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 17 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:66:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 66 | struct LessPosLen : public ::std::binary_function < TPosLen, TPosLen, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:81:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 81 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:129:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 129 | struct LessId : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:142:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 142 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:165:40: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 165 | struct LessGPosEnd : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:184:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 184 | struct LessGPosEndOa : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:206:36: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct HigherQ : public ::std::binary_function < TQual, TQual, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1189 | return begin(me, tag_) + pos; /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1387:36: required from ‘void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1387 | TContigGapIter refIt = iter(referenceGaps,candidateViewPos-refStart); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:765:36: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 765 | doSnpAndMethCalling(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, false, vcfStream, bedStream, methOptions, options); //bs /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 1286 | int result = detectSNPs(options, methOptions); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1180:37: required from ‘TStream& seqan::operator<<(TStream&, const Gaps&) [with TStream = std::basic_ostream; TSource = String >; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1180 | stream << convert(*it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1527:47: required from ‘void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1527 | std::cout << " contigGaps: " << contigGaps << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:765:36: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 765 | doSnpAndMethCalling(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, false, vcfStream, bedStream, methOptions, options); //bs /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:75, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1180:37: required from ‘TStream& seqan::operator<<(TStream&, const Gaps&) [with TStream = std::basic_ostream; TSource = String >; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1180 | stream << convert(*it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1527:47: required from ‘void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1527 | std::cout << " contigGaps: " << contigGaps << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:765:36: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 765 | doSnpAndMethCalling(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, false, vcfStream, bedStream, methOptions, options); //bs /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1180:37: required from ‘TStream& seqan::operator<<(TStream&, const Gaps&) [with TStream = std::basic_ostream; TSource = String >; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1180 | stream << convert(*it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1527:47: required from ‘void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1527 | std::cout << " contigGaps: " << contigGaps << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:765:36: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 765 | doSnpAndMethCalling(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, false, vcfStream, bedStream, methOptions, options); //bs /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1157:36: required from ‘void seqan::write(TFile&, const Gaps&, const TIDString&, Raw) [with TFile = std::basic_ostream; TSource = String >; TIDString = char [1]; TSpec = AnchorGaps, Alloc<> > >; Raw = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1157 | streamPut(target, convert(*begin_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2110:7: required from ‘void seqan::_printRead(TStream&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2110 | write(stream, readGaps, "", format); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1195:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1195 | printAlignment(std::cout, Raw(), layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1157:36: required from ‘void seqan::write(TFile&, const Gaps&, const TIDString&, Raw) [with TFile = std::basic_ostream; TSource = String >; TIDString = char [1]; TSpec = AnchorGaps, Alloc<> > >; Raw = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1157 | streamPut(target, convert(*begin_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2110:7: required from ‘void seqan::_printRead(TStream&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 2110 | write(stream, readGaps, "", format); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1195:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1195 | printAlignment(std::cout, Raw(), layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:343:54: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 343 | TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = const Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = const Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:1157:36: required from ‘void seqan::write(TFile&, const Gaps&, const TIDString&, Raw) [with TFile = std::basic_ostream; TSource = String >; TIDString = char [1]; TSpec = AnchorGaps, Alloc<> > >; Raw = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1157 | streamPut(target, convert(*begin_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2110:7: required from ‘void seqan::_printRead(TStream&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2110 | write(stream, readGaps, "", format); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1195:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1195 | printAlignment(std::cout, Raw(), layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:352:96: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 352 | if (lastWasGap != inGap || inGap != static_cast(isGap(cit)) || (!inGap && convert(*cit) != convert(*it))) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:352:96: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 352 | if (lastWasGap != inGap || inGap != static_cast(isGap(cit)) || (!inGap && convert(*cit) != convert(*it))) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:352:119: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 352 | if (lastWasGap != inGap || inGap != static_cast(isGap(cit)) || (!inGap && convert(*cit) != convert(*it))) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 211 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 99 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:352:119: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 352 | if (lastWasGap != inGap || inGap != static_cast(isGap(cit)) || (!inGap && convert(*cit) != convert(*it))) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:99:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:106:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 106 | : data_iterator(_other.data_iterator) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:680:15: required from ‘int readMatchesFromSamBam(TSetContigAnchorGaps&, TReader&, seqan::BamIOContext&, seqan::BamAlignmentRecord&, TFragmentStore&, TFragmentStore&, TContigId, TContigPos, TContigPos, TOptions&) [with TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TReader = seqan::RecordReader, seqan::SinglePass >; TNameStore = seqan::StringSet > >; TFragmentStore = seqan::FragmentStore; TContigId = int; TContigPos = long int; TOptions = SNPCallingOptions; typename seqan::Value::Type = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 680 | TRead curr_read = record.seq; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:697:47: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 697 | int result = readMatchesFromSamBam(setContigAnchorGaps, *recordReaders[j], contexts[j], records[j], fragmentStoreTmp, fragmentStore1, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 698 | currContigId, currentWindowBegin, currentWindowEnd, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:352:96: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 352 | if (lastWasGap != inGap || inGap != static_cast(isGap(cit)) || (!inGap && convert(*cit) != convert(*it))) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:211:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 211 | return TProxy(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_base.h:297:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 297 | return value(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_svg.h:352:119: required from ‘void seqan::_printRead(SVGFile&, const Tag&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TFormatTag = TagRaw_; TContigGaps = Gaps >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 352 | if (lastWasGap != inGap || inGap != static_cast(isGap(cit)) || (!inGap && convert(*cit) != convert(*it))) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2278:14: required from ‘void seqan::printAlignment(TStream&, const Tag&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = SVGFile; TFormatTag = TagRaw_; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2278 | _printRead(stream, format, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_consensus_realign.h:633:27: required from ‘void reAlign(seqan::FragmentStore&, TId, TBandwidth, bool, TOptions&, const TModel&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TId = int; TBandwidth = int; TOptions = MethCallingOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 633 | printAlignment(svg, Raw(), layout, fragStore, 0, (TContigPos)0, (TContigPos)200, 0, 300); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_realignment.h:245:12: required from ‘void doRealigning(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 245 | reAlign(fragmentStore, 0, bandWidth, true, methOptions, BsSimple()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.h:1231:29: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1231 | doRealigning(fragStoreGroup, groupWindowBegin, groupWindowBegin, methOptions, options); // TODO: do only for reads spanning potential indel position /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:752:35: required from ‘bool detectSNPsForContig(TVcfStream&, TBedStream&, seqan::FragmentStore&, TContigId&, TReaders&, TContexts&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TVcfStream = seqan::VcfStream; TBedStream = seqan::BedStream; TSpec = seqan::SnpStoreSpec_; TContigId = int; TReaders = seqan::String, seqan::SinglePass >*>; TContexts = seqan::String > > > >; TRecords = seqan::String; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 752 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfStream, bedStream, methOptions, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:919:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 919 | detectSNPsForContig(tempVcfStream, tempBedStream, fragmentStore1, currContigId, recordReaders, contexts, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar.cpp:1286:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1286 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/proxy_iterator.h:100:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 100 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:56, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorRead(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps >, AnchorGaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:534:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 534 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:535:13: note: here 535 | case 'I': | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorContig(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:564:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 564 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:565:13: note: here 565 | case 'D': | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h: In function ‘void seqan::assignTargetFreqs(Score >&, const TString&, TMethOptions&, BsTop&) [with TValue = double; TString = String, double> >; TBsProfileScore = const Tag; TModel = Tag; TCellDescriptor = Tag; TMethOptions = MethCallingOptions]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:190:38: warning: this statement may fall through [-Wimplicit-fallthrough=] 190 | me.targetFreqs[i][3] += ((1.0-estMethLevel)/sum)/4.0; // T | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:191:13: note: here 191 | case -1: // Ref gap | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h: In function ‘void seqan::assignTargetFreqs(Score >&, const TString&, TMethOptions&, BsTop&) [with TValue = double; TString = String, double> >; TBsProfileScore = const Tag; TModel = Tag; TCellDescriptor = Tag; TMethOptions = MethCallingOptions]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:190:38: warning: this statement may fall through [-Wimplicit-fallthrough=] 190 | me.targetFreqs[i][3] += ((1.0-estMethLevel)/sum)/4.0; // T | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:191:13: note: here 191 | case -1: // Ref gap | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h: In function ‘void seqan::assignTargetFreqs(Score >&, const TString&, TMethOptions&, BsBottom&) [with TValue = double; TString = String, double> >; TBsProfileScore = const Tag; TModel = Tag; TCellDescriptor = Tag; TMethOptions = MethCallingOptions]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:265:38: warning: this statement may fall through [-Wimplicit-fallthrough=] 265 | me.targetFreqs[i][3] += (1.0/sum)/4.0; // T | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:266:13: note: here 266 | case -1: // Ref gap | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h: In function ‘void seqan::assignTargetFreqs(Score >&, const TString&, TMethOptions&, BsBottom&) [with TValue = double; TString = String, double> >; TBsProfileScore = const Tag; TModel = Tag; TCellDescriptor = Tag; TMethOptions = MethCallingOptions]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:265:38: warning: this statement may fall through [-Wimplicit-fallthrough=] 265 | me.targetFreqs[i][3] += (1.0/sum)/4.0; // T | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_score.h:266:13: note: here 266 | case -1: // Ref gap | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:351:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:352:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:353:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:354:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:361:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:362:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:363:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:364:22, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:351:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:352:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:353:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:354:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:361:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:362:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:363:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = long double; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = long double; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = long double; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = long double; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const Naive&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:364:22, inlined from ‘void adjustConstantsSize(TConstantSet&, TStrand, const LogFunction&) [with TConstantSet = seqan::String > >; TStrand = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘void constructConstantsAndLHoods(TConstantSet&, TLHoods&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TMethOptions&, TRefContext&, const TMethod&) [with TConstantSet = seqan::String > >; TLHoods = seqan::String; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TMethOptions = MethCallingOptions; TRefContext = RefContext; TMethod = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void getCandidateProbs(TProbs&, TBetas&, TMethOptions&, TOptions&, TQStrings&, TQStrings&, TMapqs&, TMapqs&, TOriginString&, TOriginString&, TCounts&, TCounts&, TRefContext&) [with TProbs = seqan::String; TBetas = seqan::String; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; TQStrings = seqan::String > >; TMapqs = seqan::String >; TOriginString = seqan::String >; TCounts = seqan::String >; TRefContext = RefContext]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 35%] Linking CXX executable ../../../bin/casbar cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/casbar.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/casbar.dir/casbar.cpp.o -o ../../../bin/casbar -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 35%] Built target casbar make -f extras/apps/bs_tools/CMakeFiles/four2three.dir/build.make extras/apps/bs_tools/CMakeFiles/four2three.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/bs_tools/CMakeFiles/four2three.dir/build.make extras/apps/bs_tools/CMakeFiles/four2three.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 35%] Building CXX object extras/apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o -MF CMakeFiles/four2three.dir/four2three.cpp.o.d -o CMakeFiles/four2three.dir/four2three.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.cpp:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.cpp:40: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.h:14:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 14 | struct ConvertCT : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.h:23:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 23 | struct ConvertGA : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools/four2three.cpp:36: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 37%] Linking CXX executable ../../../bin/four2three cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/four2three.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/four2three.dir/four2three.cpp.o -o ../../../bin/four2three -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 37%] Built target four2three make -f extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 37%] Building CXX object extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -MF CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o.d -o CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_bam_coverage.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_bam_coverage.cpp:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_bam_coverage.cpp:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_bam_coverage.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:426:11: required from ‘int seqan::readRegion(String&, const FaiIndex&, unsigned int, unsigned int, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 426 | resize(str, toRead, TValue()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:505:22: required from ‘int seqan::readSequence(String&, const FaiIndex&, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 505 | return readRegion(str, index, refId, 0, sequenceLength(index, refId)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_bam_coverage.cpp:219:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 219 | if (readSequence(contigSeq, faiIndex, i) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 38%] Linking CXX executable ../../../bin/fx_bam_coverage cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_bam_coverage.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -o ../../../bin/fx_bam_coverage -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 38%] Built target fx_bam_coverage make -f extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 38%] Building CXX object extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -MF CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o.d -o CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_fastq_stats.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_fastq_stats.cpp:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_fastq_stats.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_fastq_stats.cpp:39: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:580:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, TQualString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String, Alloc<> >; TQualString = String >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 580 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:458:40: required from ‘int seqan::SequenceStreamImpl_::readRecord(TId&, TSequence&, TQualities&, const TFormatTag&) [with TId = seqan::String >; TSequence = seqan::String, seqan::Alloc<> >; TQualities = seqan::String >; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 458 | res = seqan::readRecord(id, seq, qual, *_mmapReaderDoublePass, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:680:38: required from ‘int seqan::readRecord(TId&, TSequence&, TQualities&, SequenceStream&) [with TId = String >; TSequence = String, Alloc<> >; TQualities = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 680 | res = seqIO._impl->readRecord(id, seq, qual, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools/fx_fastq_stats.cpp:303:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 303 | if (readRecord(id, seq, quals, inStream) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/new_allocator.h:34, from /usr/include/c++/14/ppc64le-redhat-linux/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/stl_tree.h:64: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 38%] Linking CXX executable ../../../bin/fx_fastq_stats cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_fastq_stats.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -o ../../../bin/fx_fastq_stats -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 38%] Built target fx_fastq_stats make -f extras/apps/gustaf/CMakeFiles/gustaf.dir/build.make extras/apps/gustaf/CMakeFiles/gustaf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/gustaf /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/gustaf/CMakeFiles/gustaf.dir/build.make extras/apps/gustaf/CMakeFiles/gustaf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 40%] Building CXX object extras/apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/gustaf && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -MF CMakeFiles/gustaf.dir/gustaf.cpp.o.d -o CMakeFiles/gustaf.dir/gustaf.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:28, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf.cpp:27: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf.cpp:24: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seeds.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:30: /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_types.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_types.h:154:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | struct LessPos : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_types.h:206:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct LessLength : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/parse_lm.h:47, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/create_stellarmatches_from_file.h:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer.h:44, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_parseOptions.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf.cpp:28: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_out.h:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf.cpp:30: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:688:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 688 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf.cpp:25: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:701:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 701 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 151 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:152:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 152 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:688:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 688 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:151:46: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:199:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 199 | TAlign ali(align); | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:89: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:252:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 252 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:587:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 587 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:444:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 444 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:185:17: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 185 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Dependent >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = BucketMap; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet, Alloc<> >, Dependent > >; TShapeSpec = UngappedShape<0>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Dependent > >; TSpec = IndexQGram, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:185:17: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 185 | indexRequire(qgramIndex, QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:206: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:785:16: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 785 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:809:19: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 809 | integrateAlign(align, localAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:101: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:244:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 244 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:780:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align::Type, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 780 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:809:19: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 809 | integrateAlign(align, localAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_type.h:437:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 437 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TVertexDescriptor = unsigned int; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1917:15: required from ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TValue, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1917 | findIntervals(g, pm, act_knot, query_begin, query_end, result); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1898:15: required from ‘void seqan::findIntervals(const IntervalTree&, TValue, TValue, String&) [with TValue = unsigned int; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1898 | findIntervals(tree.g,tree.pm,query_begin,query_end,result); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf_matepairs.h:240:18: required from ‘bool _checkRightMateMatches(const TMatch&, const seqan::String&, const TMSplazerChain&, const MSplazerOptions&) [with TMatch = StellarMatch, seqan::Alloc<> >, seqan::String > >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 240 | findIntervals(gustafChain.rightMateTree, mateIntervalBegin, mateIntervalEnd, confMateMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf_matepairs.h:278:42: required from ‘bool _checkMateMatches(const TMatch&, const seqan::String&, const TMSplazerChain&, const MSplazerOptions&) [with TMatch = StellarMatch, seqan::Alloc<> >, seqan::String > >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 278 | return _checkRightMateMatches(sMatch, queryMatches, gustafChain, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf_matepairs.h:345:35: required from ‘void _initialiseGraphMatePairs(QueryMatches >&, TMSplazerChain&, const MSplazerOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 345 | if (!_checkMateMatches(queryMatches.matches[i], queryMatches.matches, chain, options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_algorithms.h:644:42: required from ‘void _chainQueryMatches(seqan::StringSet > >&, seqan::String&, seqan::String&, const seqan::StringSet >&, seqan::StringSet >&, seqan::String >&, const MSplazerOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TScoreAlloc = seqan::String; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 644 | _initialiseGraphMatePairs(stellarMatches[i], chain, msplazerOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:224:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 224 | _chainQueryMatches(stellarMatches, distanceScores, queryChains, queryIDs, queries, readJoinPositions, msplazerOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1949:26: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1949 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1961:43: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1961 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1982:51: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1982 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:447:13: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 447 | return host(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:698:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 698 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h: In instantiation of ‘void seqan::integrateAlign(Align&, const Align&, const String&) [with TSource1 = String, Alloc<> >; TSpec1 = Tag; TSource2 = Segment, Alloc<> >, InfixSegment>; TSpec2 = Tag; TPos = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:154:19: required from ‘void seqan::integrateAlign(Align&, const Align::Type, TSpec2>&) [with TSource = String, Alloc<> >; TSpec1 = Tag; TSpec2 = Tag; typename Infix::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 154 | integrateAlign(align, infixAlign, viewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:620:16: required from ‘void _tracebackLeft(const TMatrix&, const TCoord&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, TPos, TPos, TAlign&) [with TMatrix = seqan::String >; TCoord = seqan::Pair; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TPos = long unsigned int; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 620 | integrateAlign(align, infixAlign); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:753:17: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 753 | _tracebackLeft(matrixLeft, (*endPair.i1).coord, infH, infV, seed, seedOld, endLeftH, endLeftV, align); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/alignment_operations.h:124:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 124 | it = iter(row(align, i), value(viewPos, i)); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer.h:121:8: required from ‘bool _writeGlobalBreakpoints(const seqan::String&, seqan::StringSet >&, seqan::StringSet&, const MSplazerOptions&, seqan::Vcf) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::Vcf = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 121 | struct Breakpoint /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:271:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: 271 | _writeGlobalBreakpoints(globalBreakpoints, databases, databaseIDs, msplazerOptions, Vcf()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_array.h:91:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:222:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 222 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11: required from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String, Alloc<> >; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1608 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf_matepairs.h:177:15: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 177 | append(seq, seqL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:72:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 72 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, shortQueryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_array.h:401:10: required from ‘void seqan::assignSource(Gaps >&, const TSequence2&) [with TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequence2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 401 | value(gaps._source) = source; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:614:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 614 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> >, InfixSegment>, Owner<> >; TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:402:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 402 | appendValue(str, infixH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:703:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 703 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11: required from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String, Alloc<> >; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1608 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/gustaf_matepairs.h:177:15: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 177 | append(seq, seqL); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:72:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 72 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, shortQueryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:703:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 703 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:703:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 703 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar_extension.h:860:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 860 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:643:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 643 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Triple; TSource = Triple]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:268:11: required from ‘void seqan::move(TTarget&, TSource&) [with TTarget = Triple; TSource = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 268 | assign(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1056:13: required from ‘void seqan::_arrayMoveForwardDefault(TSource1, TSource2, TTarget) [with TTarget = Triple*; TSource1 = Triple*; TSource2 = Triple*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1056 | move(*target_begin, *source_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1600:29: required from ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, False) [with TValue = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1600 | _arrayMoveForwardDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1211:25: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = Triple*; TSource1 = Triple*; TSource2 = Triple*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1211 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1295:22: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1929:12: required from ‘void seqan::replace(TTarget&, TPositionBegin, TPositionEnd, const TSource&) [with TTarget = String, Alloc<> >; TPositionBegin = int; TPositionEnd = int; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1929 | replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:224:20: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 224 | replace(queue, 0, 2, String()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:624:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 624 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 716 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/msplazer_main.h:145:27: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 145 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘constexpr seqan::Triple& seqan::Triple::operator=(const seqan::Triple&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:57: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: because ‘seqan::Triple’ has user-provided ‘seqan::Triple::Triple(const seqan::Triple&) [with T1 = long unsigned int; T2 = long unsigned int; T3 = int; TSpec = void]’ 162 | inline Triple(Triple const & _p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = ScoreAndID; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = ScoreAndID; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = ScoreAndID; TLess = std::less >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::pop(PriorityType&) [with TValue = ScoreAndID; TLess = std::less >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = ScoreAndID; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = ScoreAndID; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = ScoreAndID; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = ScoreAndID; TLess = std::less >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘typename seqan::LocalAlignmentFinder::TMatrixPosition seqan::_getNextBestEndPosition(LocalAlignmentFinder&, TScoreValue) [with TScoreValue = int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_waterman_eggert_impl.h:673:8, inlined from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:572:39, inlined from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_enumeration_banded.h:109:35, inlined from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_enumeration_banded.h:121:30, inlined from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:617:30, inlined from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf/../../../core/apps/stellar/stellar.h:716:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 40%] Linking CXX executable ../../../bin/gustaf cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/gustaf.dir/gustaf.cpp.o -o ../../../bin/gustaf -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 40%] Built target gustaf make -f extras/apps/insegt/CMakeFiles/insegt.dir/build.make extras/apps/insegt/CMakeFiles/insegt.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/insegt /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/insegt/CMakeFiles/insegt.dir/build.make extras/apps/insegt/CMakeFiles/insegt.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 41%] Building CXX object extras/apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/insegt && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o -MF CMakeFiles/insegt.dir/insegt.cpp.o.d -o CMakeFiles/insegt.dir/insegt.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:14: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:16: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:21: /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/create_gff.h: In function ‘void seqan::createAnnoCountGFF(TFile&, TAnnoCountStore&, TAnnoNormStore&, FragmentStore&, TMap&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/create_gff.h:225:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 225 | if (getValue(itAnno).typeId != INVALID_ID) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/create_gff.h:228:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 228 | if (getValue(itAnno).contigId == INVALID_ID ) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:23: /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h: In function ‘bool seqan::ngsOverlapper(TOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:901:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 901 | if (!readOutput.good()) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 903 | createReadCountGFF(readOutput, readAnnoStore, fragStore); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:908:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 908 | if (!annoOutput.good()) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:910:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 910 | createAnnoCountGFF(annoOutput, annoCountStore, annoNormStore, fragStore, mapO); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:915:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 915 | if (!tupleOutput.good()) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:917:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 917 | createTupleCountGFF(tupleOutput, tupleCountStore, fragStore, options.thresholdCount, options.thresholdRPKM); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp: In function ‘int main(int, const char**)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:188:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 188 | if (res != ArgumentParser::PARSE_OK) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 191 | if (options.maxTuple) | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h: In instantiation of ‘seqan::Iter > seqan::nodeDown(const Iter >&) [with TFragmentStore = FragmentStore<>; TSpec = void]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:45:64: required from ‘void seqan::adjustParentEntries(FragmentStore&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: 45 | getAnnotation(it).contigId = getAnnotation(nodeDown(it)).contigId; // If no child exists: nothing happens /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:865:21: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: 865 | adjustParentEntries(fragStore); /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:191:9: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:1281:54: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)’ is deprecated [-Wdeprecated-copy] 1281 | Iter > tmp(it); | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: because ‘seqan::Iter, seqan::AnnotationTree<> >’ has user-provided ‘const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]’ 415 | operator = (Iter const &_origin) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:1283:16: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)’ is deprecated [-Wdeprecated-copy] 1283 | return tmp; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: because ‘seqan::Iter, seqan::AnnotationTree<> >’ has user-provided ‘const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]’ 415 | operator = (Iter const &_origin) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_intervaltree.h:182:15: required from ‘void seqan::findIntervalsForInterval(String&, TIntervalTree&, TInterval&, const unsigned int&) [with TIntervalTree = IntervalTree; TInterval = Interval; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: 182 | findIntervals(intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval, result1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:82:27: required from ‘void seqan::getIdsForRead(TAnnoIds&, FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TIntervalTree = IntervalTree; TIntervals = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: 82 | findIntervalsForInterval(value(itR), intervalTree, getValue(itI), offsetInterval); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/fusion.h:775:18: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: 775 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:884:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: 884 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_annotation.h:415:9: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1827:26: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1827 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1838:43: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1838 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1859:51: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1859 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1189 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_anchor.h:465:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 465 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2801:19: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 2801 | insertGaps(gaps, insPos - rBegin, blkLen); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:459:45: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 459 | convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:838:6: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 838 | read(fileSAM, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:12: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2738:18: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 2738 | TContigGapsPW contigGapsPW(/*contigInfix, */gaps[(*it).id]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:459:45: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 459 | convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:838:6: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 838 | read(fileSAM, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:13: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder >, InfixSegment>, Tag >; TValue = Segment >, InfixSegment>; typename Value::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment >, InfixSegment>; TValue2 = const Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1018:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment >, InfixSegment>; TSource = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1018 | create(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:153:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2739:15: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2739 | TReadGaps readGaps(store.readSeqStore[(*it).readId], (*it).gaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:459:45: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 459 | convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:838:6: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 838 | read(fileSAM, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String >, GapAnchor, void>, Alloc<> >; TValue = ContigStoreElement >, GapAnchor, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1117:14: required from ‘void seqan::_storeAppendContig(FragmentStore&, TId&, TName&) [with TSpec = void; TConfig = FragmentStoreConfig; TId = unsigned int; TName = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1117 | appendValue(fragStore.contigStore, TContigElement()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_gff.h:256:23: required from ‘void seqan::_storeOneAnnotation(TFragmentStore&, IOContextGff_&) [with TFragmentStore = FragmentStore<>; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 256 | _storeAppendContig(fragStore, ctx.annotation.contigId, ctx.contigName); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_gff.h:331:32: required from ‘void seqan::read(TFile&, FragmentStore&, Gff) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Gff = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 331 | _storeOneAnnotation(fragStore, ctx); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:861:10: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 861 | read(fileGFF, fragStore, Gff()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:577:30: required from ‘void seqan::_readAlignments(TStreamOrReader&, BamIOContext&, FragmentStore&, TContigAnchorGaps&, TMatchMateInfos&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > >, String > >; TSpec = void; TConfig = FragmentStoreConfig; TContigAnchorGaps = StringSet, Alloc<> >, Owner > >; TMatchMateInfos = String, Alloc<> >; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 577 | _readOneAlignment(streamOrReader, bamIOContext, fragStore, contigAnchorGaps, matchMateInfos, contextSAM, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 578 | importFlags, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:452:24: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 452 | _readAlignments(streamOrReader, bamIOContext, fragStore, contigAnchorGaps, matchMateInfos, tag, importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:838:6: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 838 | read(fileSAM, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:577:30: required from ‘void seqan::_readAlignments(TStreamOrReader&, BamIOContext&, FragmentStore&, TContigAnchorGaps&, TMatchMateInfos&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > >, String > >; TSpec = void; TConfig = FragmentStoreConfig; TContigAnchorGaps = StringSet, Alloc<> >, Owner > >; TMatchMateInfos = String, Alloc<> >; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 577 | _readOneAlignment(streamOrReader, bamIOContext, fragStore, contigAnchorGaps, matchMateInfos, contextSAM, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 578 | importFlags, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:452:24: required from ‘void seqan::_readImpl(TStreamOrReader&, FragmentStore&, const TTag&, const FragStoreImportFlags&) [with TStreamOrReader = RecordReader, SinglePass >; TSpec = void; TConfig = FragmentStoreConfig; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 452 | _readAlignments(streamOrReader, bamIOContext, fragStore, contigAnchorGaps, matchMateInfos, tag, importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:474:18: required from ‘void seqan::read(TFile&, FragmentStore&, Sam, const FragStoreImportFlags&) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 474 | _readImpl(reader, fragStore, Sam(), importFlags); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:496:13: required from ‘void seqan::read(TFile&, FragmentStore&, Sam) [with TFile = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 496 | read(file, fragStore, Sam(), FragStoreImportFlags()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/overlap_module.h:838:6: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 838 | read(fileSAM, fragStore, Sam()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt/insegt.cpp:197:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | ngsOverlapper(options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:56, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorRead(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps >, InfixSegment>, AnchorGaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:534:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 534 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:535:13: note: here 535 | case 'I': | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorRead(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:534:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 534 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:535:13: note: here 535 | case 'I': | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h: In function ‘unsigned int seqan::cigarToGapAnchorContig(const TCigarString&, TGaps&) [with TCigarString = String >; TGaps = Gaps, Alloc<> > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:564:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 564 | insertGaps(it, cigar[i].count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/cigar.h:565:13: note: here 565 | case 'D': | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 41%] Linking CXX executable ../../../bin/insegt cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/insegt && /usr/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/insegt.dir/insegt.cpp.o -o ../../../bin/insegt -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 41%] Built target insegt make -f extras/apps/mason2/CMakeFiles/mason_sim.dir/build.make extras/apps/mason2/CMakeFiles/mason_sim.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_sim.dir/build.make extras/apps/mason2/CMakeFiles/mason_sim.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 43%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -MF CMakeFiles/mason_sim.dir/external_split_merge.cpp.o.d -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/external_split_merge.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/external_split_merge.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/external_split_merge.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/external_split_merge.h:49: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -MF CMakeFiles/mason_sim.dir/genomic_variants.cpp.o.d -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:53, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:52: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.h:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = int; TCargo = GenomicInterval]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1886:15: required from ‘void seqan::findIntervals(const IntervalTree&, TValue, String&) [with TValue = int; TCargo = GenomicInterval]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1886 | findIntervals(it.g,it.pm,query,result); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.cpp:644:18: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 644 | findIntervals(svIntervalTree, svPos, intervals); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1827:26: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1827 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1838:43: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1838 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1859:51: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1859 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.cpp:234:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 234 | append(seq, infix(contig, lastPos, snpRecord.pos)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1477:56: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = const seqan::SimpleType; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1477 | typename Size::Type new_length = reserve(me, me_length + 1, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TValue = SimpleType; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.cpp:246:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 246 | appendValue(seq, snpRecord.to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String, Alloc<> >; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.cpp:234:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 234 | append(seq, infix(contig, lastPos, snpRecord.pos)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ [ 45%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -MF CMakeFiles/mason_sim.dir/mason_options.cpp.o.d -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_options.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_options.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_options.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 45%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -MF CMakeFiles/mason_sim.dir/methylation_levels.cpp.o.d -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:39: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >; TValue = String >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = String >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = String >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = String >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = String >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = String >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = String >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::HtmlToolDocPrinter_::_toHtml(const TSequence&) const [with TSequence = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/tool_doc.h:284:34: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::HtmlToolDocPrinter_::_toHtml(const TSequence&) const [with TSequence = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 46%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_454.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_454.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_454.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1477:56: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = const seqan::SimpleType; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1477 | typename Size::Type new_length = reserve(me, me_length + 1, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TValue = SimpleType; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_454.cpp:372:24: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 372 | appendValue(seq, seqan::Dna(i % 4)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = CigarElement<>; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = CigarElement<>; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘std::pair appendOperation(TCigarString&, char)’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:365:22: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/stdexcept:38: /usr/include/c++/14/new: In function ‘std::pair appendOperation(TCigarString&, char)’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_base.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_base.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_base.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_genome.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.h:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1477:56: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = const char; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1477 | typename Size::Type new_length = reserve(me, me_length + 1, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TValue = char; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >; TValue = char]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.cpp:69:28: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 69 | appendValue(contig, 'A'); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:259:72: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 259 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, lenInRef)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:161:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 161 | _host(std::forward(host)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 165 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:111:7: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = seqan::Rng; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 111 | class ModifiedIterator > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:259:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 259 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, lenInRef)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:166:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 166 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:161:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 161 | _host(std::forward(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:259:72: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 259 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, lenInRef)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:670:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 670 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:452:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 452 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:193:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = seqan::Rng; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 193 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:259:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 259 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, lenInRef)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1477:56: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = const seqan::SimpleType; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1477 | typename Size::Type new_length = reserve(me, me_length + 1, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TValue = SimpleType; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:201:28: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TRead = seqan::String, seqan::Alloc<> >; TRng = seqan::Rng; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 201 | appendValue(read, *it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_illumina.cpp:257:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 257 | _simulateSequence(seq, rng, prefix(frag, lenInRef), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = CigarElement<>; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = CigarElement<>; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘std::pair appendOperation(TCigarString&, char)’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:365:22: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/stdexcept:38: /usr/include/c++/14/new: In function ‘std::pair appendOperation(TCigarString&, char)’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:146:76: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 146 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, sampleLength)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:161:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 161 | _host(std::forward(host)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 165 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:111:7: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = seqan::Rng; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 111 | class ModifiedIterator > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:146:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: 146 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, sampleLength)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:165:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_view.h:166:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 166 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:161:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 161 | _host(std::forward(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:146:76: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, sampleLength)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:670:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 670 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:452:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 452 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:59:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = seqan::Rng; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 59 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:146:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | _simulateSequence(seq, rng, TRevCompFrag(prefix(frag, sampleLength)), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1477:56: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = const seqan::SimpleType; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1477 | typename Size::Type new_length = reserve(me, me_length + 1, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TValue = SimpleType; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = String, Alloc<> >; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:67:28: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TRead = seqan::String, seqan::Alloc<> >; TRng = seqan::Rng; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 67 | appendValue(read, *it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_sanger.cpp:144:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 144 | _simulateSequence(seq, rng, prefix(frag, sampleLength), cigar); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = CigarElement<>; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = CigarElement<>; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘std::pair appendOperation(TCigarString&, char)’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:365:22: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/stdexcept:38: /usr/include/c++/14/new: In function ‘std::pair appendOperation(TCigarString&, char)’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object extras/apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -MF CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o.d -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:42: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:426:11: required from ‘int seqan::readRegion(String&, const FaiIndex&, unsigned int, unsigned int, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 426 | resize(str, toRead, TValue()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:505:22: required from ‘int seqan::readSequence(String&, const FaiIndex&, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 505 | return readRegion(str, index, refId, 0, sequenceLength(index, refId)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.cpp:268:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 268 | if (readSequence(seq, faiIndex, currRID) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 50%] Linking CXX static library libmason_sim.a cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 50%] Built target mason_sim make -f extras/apps/mason2/CMakeFiles/mason_genome.dir/build.make extras/apps/mason2/CMakeFiles/mason_genome.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_genome.dir/build.make extras/apps/mason2/CMakeFiles/mason_genome.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 50%] Building CXX object extras/apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -MF CMakeFiles/mason_genome.dir/mason_genome.cpp.o.d -o CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_genome.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_genome.cpp:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_genome.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/simulate_genome.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_genome.cpp:42: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 51%] Linking CXX executable ../../../bin/mason_genome cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_genome.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o ../../../bin/mason_genome -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 51%] Built target mason_genome make -f extras/apps/mason2/CMakeFiles/mason_methylation.dir/build.make extras/apps/mason2/CMakeFiles/mason_methylation.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_methylation.dir/build.make extras/apps/mason2/CMakeFiles/mason_methylation.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 51%] Building CXX object extras/apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -MF CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o.d -o CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_methylation.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_methylation.cpp:39: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_methylation.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_methylation.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:426:11: required from ‘int seqan::readRegion(String&, const FaiIndex&, unsigned int, unsigned int, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 426 | resize(str, toRead, TValue()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:505:22: required from ‘int seqan::readSequence(String&, const FaiIndex&, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 505 | return readRegion(str, index, refId, 0, sequenceLength(index, refId)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_methylation.cpp:166:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 166 | if (readSequence(contig, faiIndex, i) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 51%] Linking CXX executable ../../../bin/mason_methylation cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_methylation.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o ../../../bin/mason_methylation -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 51%] Built target mason_methylation make -f extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 51%] Building CXX object extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -MF CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o.d -o CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_frag_sequencing.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_frag_sequencing.cpp:39: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_frag_sequencing.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_frag_sequencing.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:501:40: required from ‘int seqan::SequenceStreamImpl_::readRecord(TId&, TSequence&, const TFormatTag&) [with TId = seqan::String >; TSequence = seqan::String, seqan::Alloc<> >; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 501 | res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:697:38: required from ‘int seqan::readRecord(TId&, TSequence&, SequenceStream&) [with TId = String >; TSequence = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 697 | res = seqIO._impl->readRecord(id, seq, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_frag_sequencing.cpp:202:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 202 | if (readRecord(fragId, fragSeq, inFragments) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 53%] Linking CXX executable ../../../bin/mason_frag_sequencing cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_frag_sequencing.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o ../../../bin/mason_frag_sequencing -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 53%] Built target mason_frag_sequencing make -f extras/apps/mason2/CMakeFiles/mason_variator.dir/build.make extras/apps/mason2/CMakeFiles/mason_variator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_variator.dir/build.make extras/apps/mason2/CMakeFiles/mason_variator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 53%] Building CXX object extras/apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp:48: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp:50: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp:1085:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 1085 | resize(tos, options.numHaplotypes, from); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String; TValue = StructuralVariantRecord; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = StructuralVariantRecord; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = StructuralVariantRecord; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = StructuralVariantRecord; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = StructuralVariantRecord; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = StructuralVariantRecord; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = StructuralVariantRecord; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘void StructuralVariantSimulator::_simulateFromSizes(Variants&, unsigned int, int, const seqan::CharString&)’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_variator.cpp:317:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551504’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void StructuralVariantSimulator::_simulateFromSizes(Variants&, unsigned int, int, const seqan::CharString&)’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 54%] Linking CXX executable ../../../bin/mason_variator cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_variator.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o ../../../bin/mason_variator -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 54%] Built target mason_variator make -f extras/apps/mason2/CMakeFiles/mason_materializer.dir/build.make extras/apps/mason2/CMakeFiles/mason_materializer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_materializer.dir/build.make extras/apps/mason2/CMakeFiles/mason_materializer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 54%] Building CXX object extras/apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -MF CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o.d -o CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp:47: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:44, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp: In member function ‘int MasonMaterializerApp::run()’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_materializer.cpp:110:33: warning: catching polymorphic type ‘class MasonIOException’ by value [-Wcatch-value=] 110 | catch (MasonIOException e) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 56%] Linking CXX executable ../../../bin/mason_materializer cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_materializer.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -o ../../../bin/mason_materializer -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 56%] Built target mason_materializer make -f extras/apps/mason2/CMakeFiles/mason_simulator.dir/build.make extras/apps/mason2/CMakeFiles/mason_simulator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_simulator.dir/build.make extras/apps/mason2/CMakeFiles/mason_simulator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 58%] Building CXX object extras/apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -MF CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o.d -o CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/fragment_generation.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:47: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/random.h:46, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/fragment_generation.h:50: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_array.h:243:34: required from ‘void seqan::_reinitArrayGaps(Gaps >&) [with TSequence = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 243 | _setLength(gaps, length(value(gaps._source))); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_array.h:153:25: required from ‘seqan::Gaps >::Gaps(TSequence&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 153 | _reinitArrayGaps(*this); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:221:57: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: 221 | seqan::Gaps gapsContig(contigInfix); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/fragment_generation.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:476:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 476 | TConstSeqHIterator seqHIter = begin(seqH, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 686 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1205:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1205 | TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:619:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 619 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1206:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBand_ >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1206 | TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1421:32: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:476:40: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 476 | TConstSeqHIterator seqHIter = begin(seqH, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:686:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 686 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:477:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_ >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 477 | TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_algorithm_impl.h:1419:34: required from ‘typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBand_&, const DPProfile_&) [with TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; typename Value::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1419 | _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:675:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TDPScoutStateSpec = Tag; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 675 | return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_(lowerDiagonal, upperDiagonal), TDPProfile()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:716:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&, const TGapsTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; TGapsTag = TracebackConfig_, Tag >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 716 | return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717 | upperDiagonal, algoTag, gapsTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/dp_setup.h:732:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, const TSequenceH&, const TSequenceV&, const Score&, const TAlignConfig&, int, int, const TAlgoTag&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue = int; TScoreSpec = Tag; TAlignConfig = AlignConfig<>; TAlgoTag = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 732 | return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 | algoTag, TracebackConfig_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:172:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 172 | TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 | lowerDiag, upperDiag, algoTag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:209:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 209 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_banded.h:226:27: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 226 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:229:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 229 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, lDiag, uDiag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type, const TValue&) [with T = seqan::String, seqan::Alloc<> >; TValue = seqan::SimpleType; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1925 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1964:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, const TValue2&, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = unsigned int; TValue2 = SimpleType; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1964 | return _Resize_String >::resize_(me, new_length, val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String, Alloc<> >; TSize = unsigned int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:426:11: required from ‘int seqan::readRegion(String&, const FaiIndex&, unsigned int, unsigned int, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 426 | resize(str, toRead, TValue()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:505:22: required from ‘int seqan::readSequence(String&, const FaiIndex&, unsigned int) [with TValue = SimpleType; TSpec = Alloc<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 505 | return readRegion(str, index, refId, 0, sequenceLength(index, refId)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_simulator.cpp:817:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 817 | if (readSequence(refSeq, vcfMat.faiIndex, rID) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/new_allocator.h:34, from /usr/include/c++/14/ppc64le-redhat-linux/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 58%] Linking CXX executable ../../../bin/mason_simulator cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_simulator.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -o ../../../bin/mason_simulator -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 58%] Built target mason_simulator make -f extras/apps/mason2/CMakeFiles/mason_splicing.dir/build.make extras/apps/mason2/CMakeFiles/mason_splicing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_splicing.dir/build.make extras/apps/mason2/CMakeFiles/mason_splicing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 59%] Building CXX object extras/apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -MF CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o.d -o CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:42: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:46: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h: In function ‘int seqan::writeRecord(TStream&, const VcfRecord&, const VcfIOContext&, const Vcf&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:190:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 190 | else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/vcf_io/write_vcf.h:192:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 192 | streamWriteChar(stream, '\t'); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/vcf_materialization.h:44, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp: In member function ‘int MasonSplicingApp::run()’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: catching polymorphic type ‘class MasonIOException’ by value [-Wcatch-value=] 138 | catch (MasonIOException e) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11: required from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String, Alloc<> >; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 1608 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:292:23: required from here /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: 292 | append(transcript, buffer); /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:138:33: warning: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11: required from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String, Alloc<> >; TSource = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1608 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_splicing.cpp:292:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 292 | append(transcript, buffer); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable ../../../bin/mason_splicing cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_splicing.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -o ../../../bin/mason_splicing -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 59%] Built target mason_splicing make -f extras/apps/mason2/CMakeFiles/mason_tests.dir/build.make extras/apps/mason2/CMakeFiles/mason_tests.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/mason2/CMakeFiles/mason_tests.dir/build.make extras/apps/mason2/CMakeFiles/mason_tests.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 61%] Building CXX object extras/apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -MF CMakeFiles/mason_tests.dir/mason_tests.cpp.o.d -o CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_tests.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_tests.cpp:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/mason_tests.cpp:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = CigarElement<>; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = CigarElement<>; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = CigarElement<>; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘std::pair appendOperation(TCigarString&, char)’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:365:22, inlined from ‘std::pair appendOperation(TCigarString&, char)’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2/sequencing.h:356:28: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘std::pair appendOperation(TCigarString&, char)’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = unsigned int; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = unsigned int; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = unsigned int; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = unsigned int; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = unsigned int; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = unsigned int; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = unsigned int; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = unsigned int; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Value >::Type seqan::obtainId(IdManager&) [with TIdType = unsigned int; TSpec = Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_types/graph_idmanager.h:205:9, inlined from ‘typename seqan::VertexDescriptor > >::Type seqan::addVertex(Graph >&) [with TCargo = void; TSpec = const Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_types/graph_impl_directed.h:534:33: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘typename seqan::VertexDescriptor > >::Type seqan::addVertex(Graph >&) [with TCargo = void; TSpec = const Tag]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable ../../../bin/mason_tests cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_tests.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/mason_tests.dir/mason_tests.cpp.o -o ../../../bin/mason_tests -lrt -L/usr/lib64 -lz libmason_sim.a -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 61%] Built target mason_tests make -f extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 61%] Building CXX object extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -MF CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o.d -o CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_plot_thumbnails.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_plot_thumbnails.cpp:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_plot_thumbnails.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_plot_thumbnails.cpp:46: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable ../../../bin/roi_plot_thumbnails cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_plot_thumbnails.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -o ../../../bin/roi_plot_thumbnails -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 61%] Built target roi_plot_thumbnails make -f extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 62%] Building CXX object extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o -MF CMakeFiles/bam2roi.dir/bam2roi.cpp.o.d -o CMakeFiles/bam2roi.dir/bam2roi.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/bam2roi.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/bam2roi.cpp:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/bam2roi.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/bam2roi.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_stream.h:50, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:107: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_builder.h:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/bam2roi.cpp:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h: In function ‘void seqan::getGappedConsensus(FragmentStore&, TGappedConsensus&, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:387:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 387 | for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 389 | diff = (itGaps->gapPos - itGaps->seqPos); | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:91:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:102:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 102 | public ::std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 62%] Building CXX object extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -MF CMakeFiles/bam2roi.dir/roi_builder.cpp.o.d -o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_builder.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_builder.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_builder.cpp:35: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_builder.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io.h:54: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_builder.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_base.h:343:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 343 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h: In function ‘void seqan::njTree(const String&, Graph >&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:148:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 148 | for (unsigned i = 0; i < length(mat); ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:152:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 152 | String<__int64> av; // Average branch length to a combined node | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, StringSet&, TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:416:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 416 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:420:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 420 | TString seq; | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TNames&, FastaAlign)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:534:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 534 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:538:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 538 | String mat; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, String&, String&, const TStringSet&, const TNames&, MummerLib)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:878:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:880:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 880 | TName seq1; | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h: In function ‘void seqan::read(TFile&, Graph >&, TNames&, NewickFormat)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:985:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 985 | if (atEnd(reader)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_msa/graph_align_tcoffee_io.h:988:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 988 | TVertexDescriptor lastVertex = nilVertex; | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h: In function ‘void seqan::getGappedConsensus(FragmentStore&, TGappedConsensus&, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:387:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 387 | for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_base.h:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 389 | diff = (itGaps->gapPos - itGaps->seqPos); | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:91:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/consensus/consensus_library.h:102:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 102 | public ::std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 64%] Linking CXX executable ../../../bin/bam2roi cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam2roi.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/bam2roi.dir/bam2roi.cpp.o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -o ../../../bin/bam2roi -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 64%] Built target bam2roi make -f extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 64%] Building CXX object extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -MF CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_feature_projection.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_feature_projection.cpp:46: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_feature_projection.cpp:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/bed_io/bed_io_context.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/bed_io.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_interval.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_feature_projection.cpp:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/roi_feature_projection.cpp:43: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -MF CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_spliced.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/gff_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_spliced.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_spliced.cpp:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_spliced.h:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_spliced.h:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -MF CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_interval.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/bed_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_interval.h:42, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_interval.cpp:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi/project_interval.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/bed_io/bed_io_context.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/bed_io.h:54: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 67%] Linking CXX executable ../../../bin/roi_feature_projection cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_feature_projection.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -o ../../../bin/roi_feature_projection -lrt -L/usr/lib64 -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 67%] Built target roi_feature_projection make -f extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 67%] Building CXX object extras/apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -MF CMakeFiles/param_chooser.dir/param_chooser.cpp.o.d -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:32: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif.h:64, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:38: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif/find_motif_pms1.h: In function ‘void seqan::pms1(TStrings&, TStrings&, const TType&, const TType&, const bool&, const Oops&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif/find_motif_pms1.h:264:82: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 264 | std::count_if(vect_iter, upper_iter, std::bind2nd(std::equal_to(), *vect_iter)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif.h:66: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif/find_motif_projection.h: In function ‘void seqan::_filteringStep(TBucketAr&, TArray&, TType&, TStrings&, TPositions&, const TType&, const TType&)’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif/find_motif_projection.h:627:50: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater_equal; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 627 | bind2nd(std::greater_equal(),static_cast(s))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:33, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:40: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:29, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:34: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:712:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 712 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:740:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 740 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:766:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 766 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:784:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 784 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:806:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 806 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h: In function ‘int seqan::qualityDistributionFromPrbFile(TFile&, TDistribution&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:198:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 198 | if (skipWhitespaces(reader) != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:201:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 201 | int kickout = 0; | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h: In function ‘int seqan::qualityDistributionFromFastQIntFile(TFile&, TDistribution&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:373:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 373 | if (pm_options.verbose) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:376:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 376 | resize(avg,pm_options.totalN,(TFloat)0.0); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h: In function ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:934:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 934 | if (value(reader) == 'e') | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 938 | bool atLeastOneFound = false; | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1466:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1466 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:36: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:162: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1689:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1689 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2300:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2300 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1689:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1689 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2303 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/find_motif.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:5: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1435:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1435 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1466:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1466 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:77: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1467:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1467 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1689:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1689 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2311:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2311 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1876 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1860:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1860 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1689:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1689 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2314:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2314 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1435:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1435 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:620:11: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 620 | assignSeq(firstRead, multiFasta[0], format); // read the first sequence /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1661:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1661 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2297:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2297 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1661:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1661 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2300:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 2300 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1661:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1661 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2303 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:368:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 368 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:333:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 333 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:28: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1450:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1450 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1468:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet >, Owner > >; TMyersPatterns = String >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1468 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1694:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1694 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/readSimulator.h:433:16: required from ‘void seqan::simulateReads(TReadSet&, TReadIDs&, TGenomeSet&, int, int, TDistr&, int, int, double, bool) [with TReadSet = StringSet >, Owner > >; TReadIDs = StringSet > >; TGenomeSet = StringSet, Alloc<> > >; TDistr = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 433 | appendValue(readSet, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:755:15: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 755 | simulateReads( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^ 756 | testReads, dummyIDs, testGenome, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 757 | 50000, maxErrors+1, logErrorDistribution, 0, 0, 0.5, true); // generate 50K reads /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:18: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 793 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1724:42: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1724 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1756:13: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1756 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1774:13: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1774 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:1473:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2308:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2308 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String, Alloc<> >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/readSimulator.h:433:16: required from ‘void seqan::simulateReads(TReadSet&, TReadIDs&, TGenomeSet&, int, int, TDistr&, int, int, double, bool) [with TReadSet = StringSet >, Owner > >; TReadIDs = StringSet > >; TGenomeSet = StringSet, Alloc<> > >; TDistr = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 433 | appendValue(readSet, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:755:15: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 755 | simulateReads( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^ 756 | testReads, dummyIDs, testGenome, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 757 | 50000, maxErrors+1, logErrorDistribution, 0, 0, 0.5, true); // generate 50K reads /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:484:9: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 484 | resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:778:30: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 778 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:778:30: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 778 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2297:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2297 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:56, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, UngappedShape<0> >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, UngappedShape<0> >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2297:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2297 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2300:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2300 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, OneGappedShape>; TDir = String; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, OneGappedShape>; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, OneGappedShape>, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2300:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2300 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = True]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1593:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1593 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2303 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner >; TShape = Shape, GappedShape > >; TDir = String; TBucketMap = Nothing; TStepSize = long unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1604:25: required from ‘void seqan::createQGramIndex(TIndex&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1604 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2565:19: required from ‘bool seqan::indexCreate(Index >&, FibreSADir, Default) [with TText = StringSet >, Owner > >; TShapeSpec = Shape, GappedShape > >; TSpec = Tag; FibreSADir = const Tag; Default = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2565 | createQGramIndex(index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet >, Owner > >; TSpec = IndexQGram, GappedShape > >, Tag >; TFibre = FibreSADir_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:712:21: required from ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | indexRequire(host(pattern), QGramSADir()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1876:21: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2134:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2134 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2303:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 2303 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:778:30: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 778 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2087:9: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2087 | TIndex swiftIndex(readSet, shape); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2208:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2208 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:2297:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2297 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:830:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 830 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:1228:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1228 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/param_chooser.cpp:340:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 340 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h: In function ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:636:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 636 | ++del; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:638:33: note: here 638 | case SEQAN_INSERT: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:656:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 656 | ++del; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:658:33: note: here 658 | case SEQAN_INSERT: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h: In function ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, float>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:636:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 636 | ++del; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:638:33: note: here 638 | case SEQAN_INSERT: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:656:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 656 | ++del; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:658:33: note: here 658 | case SEQAN_INSERT: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 69%] Linking CXX executable ../../../bin/param_chooser cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../../bin/param_chooser -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 69%] Built target param_chooser make -f extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 70%] Building CXX object extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/test_param_chooser.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/test_param_chooser.cpp:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/test_param_chooser.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:33, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/test_param_chooser.cpp:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:29, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:34: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:712:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 712 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:740:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 740 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:766:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 766 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:784:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 784 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:806:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 806 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h: In function ‘int seqan::qualityDistributionFromPrbFile(TFile&, TDistribution&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:198:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 198 | if (skipWhitespaces(reader) != 0) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:201:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 201 | int kickout = 0; | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h: In function ‘int seqan::qualityDistributionFromFastQIntFile(TFile&, TDistribution&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:373:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 373 | if (pm_options.verbose) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:376:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 376 | resize(avg,pm_options.totalN,(TFloat)0.0); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h: In function ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:934:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 934 | if (value(reader) == 'e') | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 938 | bool atLeastOneFound = false; | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/test_param_chooser.cpp:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/razers.h:620:11: required from here /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: 620 | assignSeq(firstRead, multiFasta[0], format); // read the first sequence /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser/../../../core/apps/splazers/paramChooser.h:938:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 70%] Linking CXX executable ../../../bin/test_funcs_param_chooser cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../../bin/test_funcs_param_chooser make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 70%] Built target test_funcs_param_chooser make -f extras/apps/razers3/CMakeFiles/razers3.dir/build.make extras/apps/razers3/CMakeFiles/razers3.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/razers3/CMakeFiles/razers3.dir/build.make extras/apps/razers3/CMakeFiles/razers3.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 70%] Building CXX object extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -MF CMakeFiles/razers3.dir/razers.cpp.o.d -o CMakeFiles/razers3.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:57: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:63: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:33, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:845:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:862:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:896:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:934:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:968:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1009:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1046:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1087:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1130:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1174:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1218:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:75: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:127:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:83: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:264:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 264 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:320:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 320 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:365:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 365 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:48: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:89: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1312:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1312 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1315:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1315 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1312:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1312 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1315:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1315 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1312:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1312 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1315:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1315 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1364:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1364 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1312:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1312 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1364:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1364 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1315:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1315 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1364:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1364 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1367:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1367 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1312:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1312 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1367:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1367 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1315:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1315 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1367:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1367 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1370:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1370 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1312:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1312 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1370:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1370 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1315:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1315 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1370:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1370 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:101:32: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 101 | #define SEQAN_DO_PRAGMA(x) _Pragma(#x) | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/parallel/parallel_macros.h:102:33: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 102 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:697:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 697 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = FunctorGlobalEditDistAlign; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1224:33: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1224 | _writeAlignments(file, store, Sam(), FunctorGlobalEditDistAlign()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1232:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1232 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:85: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:77: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:33: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:76: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:841:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 841 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:868:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 868 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = FunctorGlobalEditDistAlign; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1224:33: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1224 | _writeAlignments(file, store, Sam(), FunctorGlobalEditDistAlign()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:90: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = FunctorGlobalEditDistAlign; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1224:33: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1224 | _writeAlignments(file, store, Sam(), FunctorGlobalEditDistAlign()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1232:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1232 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:850:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 850 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:832:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 832 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:972:32: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 972 | TSeqIter seqItEnd = end(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1232:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1232 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:777:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 777 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:34: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1087:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1087 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:462:35: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 462 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:162: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1087:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1087 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1087:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1087 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:462:35: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 462 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1087:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1087 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:32: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:924:42: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 924 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:695:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 695 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:462:35: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 462 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:2047:73: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2047 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:302:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 302 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:757:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 757 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1039:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1039 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:878:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 878 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:462:35: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 462 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:302:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 302 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:757:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 757 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1039:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1039 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:878:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 878 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:302:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 302 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:757:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 757 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1039:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1039 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:924:42: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 924 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:695:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 695 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:462:35: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 462 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:2047:73: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2047 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:878:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 878 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:462:35: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 462 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:878:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 878 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1014 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:713:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 713 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:302:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 302 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:757:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 757 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1039:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1039 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:302:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 302 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:757:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 757 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1039:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1039 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1208:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1208 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:302:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 302 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:757:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 757 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1039:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1039 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1203:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1203 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io_sam.h:1013:50: required from ‘void seqan::_writeAlignments(TFile&, FragmentStore&, Sam, const TAlignFunctor&) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignFunctor = FunctorGlobalEditDistAlign; Sam = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1013 | for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1224:33: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1224 | _writeAlignments(file, store, Sam(), FunctorGlobalEditDistAlign()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1189:28: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, Tag) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1189 | return begin(me, tag_) + pos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1169:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1169 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_anchor.h:465:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 465 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_base.h:628:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = String >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 628 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2582:18: required from ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = True]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2582 | insertGap(gaps, insPos - rBegin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1231:40: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1231 | convertMatchesToGlobalAlignment(store, scoreType, True()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:742:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 742 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:744:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 744 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 117 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:600:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment >, InfixSegment>; typename Iterator::Type>::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 600 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:971:31: required from ‘int seqan::write(TFile&, FragmentStore&, Amos) [with TFile = std::basic_ofstream; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 971 | TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1232:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1232 | write(file, store, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1309:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1309 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/outputFormat.h:1353:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 1353 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:258:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 258 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_iterator_anchor.h:117:22: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:835:14: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 835 | assignSeq(firstRead, multiFasta[0], format); // read the first sequence /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:193:23: required from ‘bool seqan::loadReads(FragmentStore&, const char*, const char*, TRazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 193 | resize(seq[j], options.trimLength); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:186:23: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 186 | if (!loadReads(store, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:616:25: required from ‘typename seqan::Iterator >::Type seqan::begin(T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 616 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:375:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 375 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:679:20: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 679 | TFilterFinderR filterFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:532:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 532 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:887:30: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Pigeonhole >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 887 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:930:28: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 930 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:695:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 695 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:896:43: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Pigeonhole >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 896 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:930:28: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 930 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:695:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 695 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:609:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 609 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:2054:30: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2054 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:887:30: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Pigeonhole >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 887 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:930:28: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 930 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:695:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 695 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1114 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:1813:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder >, InfixSegment>, Swift > > >; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1813 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:2054:30: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment >, InfixSegment>; TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2054 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:778:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 778 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1657:13: required from ‘typename seqan::Size::TMatePairStore>::Type seqan::appendMatePair(FragmentStore&, const TRead&, const TRead&, const CharString&, const CharString&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TMatePairStore>::Type = long unsigned int; typename FragmentStore::TMatePairStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1657 | appendValue(me.readSeqStore, read1, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:206:23: required from ‘bool seqan::loadReads(FragmentStore&, const char*, const char*, TRazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 206 | appendMatePair(store, seq[0], seq[1], seqId[0], seqId[1]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:186:23: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 186 | if (!loadReads(store, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:101: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:398:24: required from ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 398 | appendValue(indexText(indexL), readSetL[j]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = const Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:865:24: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | appendValue(indexText(index), store.readSeqStore[j]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1475:37: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1475 | typename Value::Type temp_copy(_value); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1925:45: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2153:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize, const TValue&) [with T = String >; TSize = int; TValue = SimpleType; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2153 | return resize(me, new_length, val, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:484:9: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 484 | resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:838:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 838 | if (!chooseParams(options, pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1657:13: required from ‘typename seqan::Size::TMatePairStore>::Type seqan::appendMatePair(FragmentStore&, const TRead&, const TRead&, const CharString&, const CharString&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TMatePairStore>::Type = long unsigned int; typename FragmentStore::TMatePairStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1657 | appendValue(me.readSeqStore, read1, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:206:23: required from ‘bool seqan::loadReads(FragmentStore&, const char*, const char*, TRazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 206 | appendMatePair(store, seq[0], seq[1], seqId[0], seqId[1]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:186:23: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 186 | if (!loadReads(store, toCString(readFileNames[0]), toCString(readFileNames[1]), options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:653:36: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 653 | TReadSet & readSetL = host(host(filterPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:81: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:841:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 841 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_reverse.h:463:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 463 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:440:24: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 440 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2241:41: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 2241 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 792 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:768:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 768 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1087:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:858:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 858 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:858:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 858 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:653:36: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 653 | TReadSet & readSetL = host(host(filterPatternL)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:1114:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:858:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 858 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:1014:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:838:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 838 | if (!chooseParams(options, pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1105:63: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = const Segment >, InfixSegment>; TNeedle2 = Segment >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1105 | typename Size::Type const columns = length(container(finder)) + state.leftClip; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1297:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TNeedle2 = const Segment >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1297 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1654:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TNeedle2 = const Segment >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1654 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1766:13: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder >, InfixSegment>, void>; TNeedle = Segment >, InfixSegment>; TNeedle2 = const Segment >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1766 | return find(finder, needle, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2177:16: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2177 | while (find(myersFinder, readPrefix, state, minScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:793:42: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 793 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_interface.h:752:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 752 | goEnd(it, container(it)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:948:7: required from ‘void seqan::goEnd(Finder&) [with THaystack = ModifiedString >, InfixSegment>, Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 948 | goEnd(hostIterator(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1656:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TNeedle2 = ModifiedString >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1656 | goEnd(finder); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1766:13: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString >, InfixSegment>, Tag >; TNeedle2 = ModifiedString >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1766 | return find(finder, needle, state); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2245:32: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSOptions<>, RazerSMode, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String >; TRead = Segment >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2245 | while (find(myersFinderRev, readRev, verifier.revPatternState, maxScore)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs.h:792:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_iterator.h:294:16: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 294 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 139 | ModifiedString(typename Parameter_::Type host) : _host(_toPointer(host)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 2948 | TReadSet & readSet = indexText(host(filterPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_string.h:139:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Pigeonhole >; TFilterFinderR = Finder >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:277:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 277 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = const seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = const Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = const Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet >, InfixSegment>, Owner<> >; TValue = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:865:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:277:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 277 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_pattern_base.h:368:14: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 368 | return value(me.data_host); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSOptions<>; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 2948 | TReadSet & readSet = indexText(host(filterPattern)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:116:15: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Swift > > >; TFilterFinderR = Finder >, InfixSegment>, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 497 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 497 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Pigeonhole >; TFilterFinderR = Finder >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:277:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 277 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:277:15: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 277 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Swift > > >; TFilterFinderR = Finder >, InfixSegment>, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 497 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 497 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: note: synthesized method ‘seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Pigeonhole >; TFilterFinderR = Finder >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Swift > > >; TFilterFinderR = Finder >, InfixSegment>, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Pigeonhole >; TFilterFinderR = Finder >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Pigeonhole >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_onegapped.h:135:17: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 135 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder >, Swift > > >; TFilterFinderR = Finder >, InfixSegment>, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:472:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder >, Swift > > >; TFilterPattern = Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSOptions<>; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 472 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:775:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_parallel.h:116:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 116 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 117 | MapSingleReads< | ~~~~~~~~~~~~~~~ 118 | TMatches_, | ~~~~~~~~~~ 119 | TFragmentStore, | ~~~~~~~~~~~~~~~ 120 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 121 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 122 | TShape, | ~~~~~~~ 123 | TOptions, | ~~~~~~~~~ 124 | TCounts, | ~~~~~~~~ 125 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_gapped.h:330:17: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 330 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1845:16: required from ‘void seqan::insertValue(T&, TPosition, const TValue&) [with T = String >; TPosition = int; TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1845 | insertValue(me, pos, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:511:16: required from ‘void seqan::initPatterns(TStateString&, const TShape&, int, const TLogErrorDistr&, TDistance, bool) [with TStateString = String, double>, Alloc<> >; TShape = String >; TLogErrorDistr = String; TDistance = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 511 | insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/shape_threshold.h:1118:14: required from ‘void seqan::qgramFilteringSensitivity(TSensitivityMatrix&, const TShape&, TPatternSize, TErrors, TThresh, TDistance, ThreshExact, const TErrorDist&) [with TSensitivityMatrix = String; TShape = Shape, GappedShape > >; TPatternSize = unsigned int; TErrors = unsigned int; TThresh = unsigned int; TDistance = Tag; TErrorDist = String; ThreshExact = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1118 | initPatterns(states, bitString, errors, logErrorDistribution, dist, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:741:42: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 741 | qgramFilteringSensitivity(sensMat, shape, totalN, maxErrors - 1, maxT - 1, HammingDistance(), ThreshExact(), logErrorDistribution); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:1310:30: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 1310 | makeSelectedStatsFile(errorDistribution, pm_options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:838:30: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: 838 | if (!chooseParams(options, pm_options)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Pigeonhole >, seqan::Finder >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, const TParam&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:363:28: required from ‘void seqan::valueConstruct(TIterator, const TParam&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 363 | TConstructor::construct(it, param_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:606:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 606 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder >, seqan::Swift > > >, seqan::Finder >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSOptions<>, seqan::String >, seqan::RazerSMode > >&)’ first required here 296 | new( (void*) & value(it) ) TNonConstValue(param_); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: required from ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 497 | class Pattern > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:296:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:277:8: required from ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 277 | class Pattern > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Finder >, InfixSegment>, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: required from ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 497 | class Pattern > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_pigeonhole.h:277:8: required from ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 277 | class Pattern > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Pigeonhole >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: required from ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 497 | class Pattern > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Finder >, InfixSegment>, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_swift.h:497:11: required from ‘void seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 497 | class Pattern > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder >, Swift > > >, Pattern >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSOptions<>, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&, RazerSMode) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:236:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 236 | int error = _mapReads(store, stats, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:865:26: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: 865 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram_openaddressing.h:159:17: note: because ‘seqan::Index >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 159 | Index(Index const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:38: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51: In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11, inlined from ‘seqan::String > seqan::_parseReadFilepath(TFile&, TChar&) [with TFile = std::basic_fstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_parsing.h:338:9, inlined from ‘int seqan::getGenomeFileNameList(CharString, StringSet > >&, RazerSOptions&) [with TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:630:60: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: In function ‘int seqan::getGenomeFileNameList(CharString, StringSet > >&, RazerSOptions&) [with TSpec = RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:613:10: note: ‘c’ declared here 613 | char c = _streamGet(file); | ^ In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]’, inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:507:30, inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:534:42, inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:541:31, inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]’ at /usr/include/c++/14/bits/stl_algobase.h:637:7, inlined from ‘void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:855:16, inlined from ‘void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:865:29, inlined from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21, inlined from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31, inlined from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1368:31, inlined from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42, inlined from ‘void seqan::append(TTarget&, TSource&) [with TTarget = String >; TSource = char]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1608:11, inlined from ‘void seqan::_parse_readShape(TFile&, TChar&, CharString&) [with TFile = std::basic_fstream; TChar = char]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:861:15, inlined from ‘bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::basic_fstream; TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:1068:25, inlined from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:1342:26: /usr/include/c++/14/bits/stl_algobase.h:438:30: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ forming offset 1 is out of the bounds [0, 1] of object ‘c’ with type ‘char’ [-Warray-bounds=] 438 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.cpp:76: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h: In function ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/paramChooser.h:1043:10: note: ‘c’ declared here 1043 | char c = _streamGet(file); | ^ [ 72%] Building CXX object extras/apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -MF CMakeFiles/razers3.dir/param_tabs.cpp.o.d -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/param_tabs.cpp [ 72%] Linking CXX executable ../../../bin/razers3 cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../../bin/razers3 -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 72%] Built target razers3 make -f extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 74%] Building CXX object extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -MF CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o.d -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/simulate_reads.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/cmdparser/cmdparser.h:39, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_cmdparser.h:36, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/simulate_reads.cpp:5: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/simulate_reads.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/simulate_reads.cpp:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/map.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/cmdparser/cmdparser.h:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:1302:14: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1302 | assignSeq(store.contigStore[seqOfs + i].seq, multiSeqFile[i], contigFile.format); // read Genome sequence /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:1323:20: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1323 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:1331:20: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1331 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/simulate_reads.cpp:114:21: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 114 | if (!loadContigs(store, getArgumentValue(parser, 0)) && (stop = true)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 74%] Linking CXX executable ../../../bin/razers3_simulate_reads cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../../bin/razers3_simulate_reads -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 74%] Built target razers3_simulate_reads make -f extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 75%] Building CXX object extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -MF CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o.d -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/cmdparser/cmdparser.h:39, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_cmdparser.h:36, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:5: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:33, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:7: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:845:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:862:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:896:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:934:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:968:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1009:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1046:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1087:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1130:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1174:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:1218:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/map.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/cmdparser/cmdparser.h:37: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1855 | _reserveStorage(seq, new_capacity, tag); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1952 | return _Resize_String >::resize_(me, new_length); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = int; typename Size::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:724:19: required from ‘bool seqan::loadReads(FragmentStore&, const char*, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 724 | resize(seq, options.trimLength); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:39:19: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 39 | if (!loadReads(store, toCString(getArgumentValue(parser, 0)), options) && (stop = true)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1887 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long int; TExpand = TagGenerous_; typename Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1952 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long int; typename Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2143 | return resize(me, new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:793:9: required from ‘void seqan::assignSeq(TSeq&, const TFastaSeq&, Fastq) [with TSeq = String, Alloc<> >; TFastaSeq = Segment >, InfixSegment>; Fastq = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 793 | resize(dst, itEnd - it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/file_format_mmap.h:1423:13: required from ‘void seqan::assignSeq(TSeq&, const TFileSeq&, const TagSelector&) [with TSeq = String, Alloc<> >; TFileSeq = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1423 | assignSeq(dst, seq, TFormatTag()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:835:14: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | assignSeq(firstRead, multiFasta[0], format); // read the first sequence /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1415:13: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, const CharString&, TId) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; TId = unsigned int; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1415 | appendValue(me.readSeqStore, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1442:19: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, const CharString&) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1442 | return appendRead(me, read, name, TReadStoreElement::INVALID_ID); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:727:19: required from ‘bool seqan::loadReads(FragmentStore&, const char*, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 727 | appendRead(store, seq, seqId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:39:19: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 39 | if (!loadReads(store, toCString(getArgumentValue(parser, 0)), options) && (stop = true)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1415:13: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, const CharString&, TId) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; TId = unsigned int; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1415 | appendValue(me.readSeqStore, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1442:19: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, const CharString&) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >; CharString = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1442 | return appendRead(me, read, name, TReadStoreElement::INVALID_ID); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:727:19: required from ‘bool seqan::loadReads(FragmentStore&, const char*, TRazerSOptions&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 727 | appendRead(store, seq, seqId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/quality2prob.cpp:39:19: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 39 | if (!loadReads(store, toCString(getArgumentValue(parser, 0)), options) && (stop = true)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3/razers.h:38: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 75%] Linking CXX executable ../../../bin/razers3_quality2prob cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../../bin/razers3_quality2prob -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 75%] Built target razers3_quality2prob make -f extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build.make extras/apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/rep_sep /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build.make extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 75%] Building CXX object extras/apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/rep_sep && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o -MF CMakeFiles/rep_sep.dir/rep_sep.cpp.o.d -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:27: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TSource = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1242:11: required from ‘void seqan::assignValue(T&, TPos, const TValue&) [with T = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TPos = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1242 | assign(value(me, pos), _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_types/graph_property.h:178:13: required from ‘void seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 178 | assignValue(pm, _getId(d), val); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:191:23: required from ‘GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; typename ReadGraph::TId = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 191 | assignProperty(me.vertexCargo, vd, new_cargo); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_construction.h:82:59: required from ‘void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 82 | TGraphCargo & new_cargo = registerRead(me, _readId(value(colIter))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:212:14: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 212 | construct(rgraph, candidates, fragStore, options.contig); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph.h:32, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:34: /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: because ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>’ has user-provided ‘GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int]’ 44 | GraphCargo(GraphCargo const& other) | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/assembly_parser.h:186:27: required from ‘void parseContig(const seqan::FragmentStore&, TId, seqan::String&, TScannerType) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int; TAnnotatedCandidateColumn = seqan::Pair > >; TScannerType = SimpleColumn]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 186 | String ungapped_seq = fragStore.readSeqStore[iter_cr->readId]; /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:198:16: required from here /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: 198 | parseContig(fragStore, options.contig, candidates, algoSpec); /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rgraph_base.h:44:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1396:13: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, TId) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; TId = unsigned int; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1396 | appendValue(me.readSeqStore, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:452:15: required from ‘int seqan::read(TFile&, FragmentStore&, Amos) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 452 | appendRead(fragStore, seq, matePairId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:155:9: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 155 | read(strmReads, fragStore, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::String >; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_concat_direct.h:318:11: required from ‘void seqan::appendValue(StringSet > >&, const TString2&, Tag) [with TString = String >; TString2 = String >; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 318 | append(me.concat, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:1396:13: required from ‘typename seqan::Size::TReadStore>::Type seqan::appendRead(FragmentStore&, const TRead&, TId) [with TSpec = void; TConfig = FragmentStoreConfig; TRead = String >; TId = unsigned int; typename Size::TReadStore>::Type = long unsigned int; typename FragmentStore::TReadStore = String, Alloc<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1396 | appendValue(me.readSeqStore, read, Generous()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_io.h:452:15: required from ‘int seqan::read(TFile&, FragmentStore&, Amos) [with TFile = _IO_FILE*; TSpec = void; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 452 | appendRead(fragStore, seq, matePairId); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:155:9: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 155 | read(strmReads, fragStore, Amos()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Triple; TSource = Triple]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:268:11: required from ‘void seqan::move(TTarget&, TSource&) [with TTarget = Triple; TSource = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 268 | assign(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1056:13: required from ‘void seqan::_arrayMoveForwardDefault(TSource1, TSource2, TTarget) [with TTarget = Triple*; TSource1 = Triple*; TSource2 = Triple*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1056 | move(*target_begin, *source_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1600:29: required from ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, False) [with TValue = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1600 | _arrayMoveForwardDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1211:25: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = Triple*; TSource1 = Triple*; TSource2 = Triple*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1211 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1295:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = Triple; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: required from ‘static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const seqan::Triple; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1367 | typename Size::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1421:42: required from ‘void seqan::append(String&, const TSource&, Tag) [with TTargetValue = Triple; TTargetSpec = Alloc<>; TSource = Triple; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1421 | AppendString_ >::append_(target, source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1626:11: required from ‘void seqan::append(TTarget&, const TSource&) [with TTarget = String >; TSource = Triple]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1626 | append(target, source, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/assembly_parser.h:197:19: required from ‘void parseContig(const seqan::FragmentStore&, TId, seqan::String&, TScannerType) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int; TAnnotatedCandidateColumn = seqan::Pair > >; TScannerType = SimpleColumn]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 197 | append(column, TAssignedReadChar(_sequenceCharacter(gapped_read[p - offset]), iter_cr->readId, _positionInRead(gapped_read[p - offset]))); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep/rep_sep.cpp:198:16: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 198 | parseContig(fragStore, options.contig, candidates, algoSpec); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘constexpr seqan::Triple& seqan::Triple::operator=(const seqan::Triple&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:57, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_base.h:162:12: note: because ‘seqan::Triple’ has user-provided ‘seqan::Triple::Triple(const seqan::Triple&) [with T1 = char; T2 = unsigned int; T3 = long unsigned int; TSpec = void]’ 162 | inline Triple(Triple const & _p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 77%] Linking CXX executable ../../../bin/rep_sep cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/rep_sep && /usr/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../../bin/rep_sep -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 77%] Built target rep_sep make -f extras/apps/searchjoin/CMakeFiles/search.dir/build.make extras/apps/searchjoin/CMakeFiles/search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin/CMakeFiles/search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/searchjoin/CMakeFiles/search.dir/build.make extras/apps/searchjoin/CMakeFiles/search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 77%] Building CXX object extras/apps/searchjoin/CMakeFiles/search.dir/search.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/searchjoin/CMakeFiles/search.dir/search.cpp.o -MF CMakeFiles/search.dir/search.cpp.o.d -o CMakeFiles/search.dir/search.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:53: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:51: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:280:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 280 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index_extras.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:44: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:321:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 321 | prepare(searcher, query); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:280:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 280 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:321:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 321 | prepare(searcher, query); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:403:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 403 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:447:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 447 | prepare(searcher, queryLong); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:403:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 403 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:447:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 447 | prepare(searcher, queryLong); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet, Alloc > >, Owner > >; TShape = Shape, UngappedShape<0> >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:280:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 280 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:126: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:103:8: warning: implicitly-declared ‘constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)’ is deprecated [-Wdeprecated-copy] 103 | struct VertexSA : public VertexEsa | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:125: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:290:17: note: because ‘seqan::VertexEsa’ has user-provided ‘seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long unsigned int]’ 290 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: synthesized method ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ first required here 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet, Alloc > >, Owner > >; TShape = Shape, UngappedShape<0> >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:280:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 280 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TShape = Shape >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet > >, Owner > >; TShape = Shape >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:403:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 403 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TShape = Shape >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet > >, Owner > >; TShape = Shape >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:403:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 403 | index(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:47: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:802:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 802 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:506:31: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 506 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘bool seqan::_moveIteratorsRight(Finder2, Index, Backtracking, TSpec> >&, const StageExact_&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:587:28: required from ‘bool seqan::_nextState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 587 | if (_moveIteratorsRight(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1277:38: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1277 | while (_nextState(finder, TStage())); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1254:14: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1254 | _find(finder, delegate, StageExact_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index_extras.h:65: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: synthesized method ‘seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >& seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >::operator=(const seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >&)’ first required here 651 | back(finder.textStack) = finder.textStack[length(finder.textStack) - 2]; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘bool seqan::_moveIteratorsRight(Finder2, Index, Backtracking, TSpec> >&, const StageExact_&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:587:28: required from ‘bool seqan::_nextState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 587 | if (_moveIteratorsRight(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1277:38: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1277 | while (_nextState(finder, TStage())); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1254:14: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1254 | _find(finder, delegate, StageExact_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: synthesized method ‘seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >& seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >::operator=(const seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >&)’ first required here 651 | back(finder.textStack) = finder.textStack[length(finder.textStack) - 2]; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:47: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:802:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 802 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:530:31: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 530 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:802:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 802 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:506:31: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 506 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:802:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 802 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:530:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 530 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:802:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 802 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:506:31: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 506 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:802:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 802 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:530:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 530 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:98: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc >; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc > >, Owner > >; TValue = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:461:16: required from ‘bool _parseText(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 461 | appendValue(parser.db.text, parser._text); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:394:50: required from ‘bool parseLine(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 394 | return _parseId(parser, reader) && _parseText(parser, reader); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:534:23: required from ‘bool load(Db&, const TFileName&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 534 | if (!parseLine(parser, reader)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:249:14: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 249 | if (!load(db, options.databaseFile)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:506:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 506 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(Pipe&, TValue&) [with TInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Skew7>; TSpec = Counter; TValue = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Skew7>, Counter>; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:386:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 386 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 387 | renamer, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 388 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:619:14: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 619 | Ref_ = *me; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc > >, Owner > >; TValue = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:461:16: required from ‘bool _parseText(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 461 | appendValue(parser.db.text, parser._text); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:394:50: required from ‘bool parseLine(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 394 | return _parseId(parser, reader) && _parseText(parser, reader); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:534:23: required from ‘bool load(Db&, const TFileName&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 534 | if (!parseLine(parser, reader)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:249:14: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 249 | if (!load(db, options.databaseFile)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:506:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 506 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc >; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc >; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Db, Alloc > >, Owner > >, Tag >; TValue2 = Db, Alloc > >, Owner > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Db, Alloc > >, Owner > >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Db, Alloc > >, Owner > >, Tag >; typename Reference > >::Type = Db, Alloc > >, Owner > >, Tag >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:797:45: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 797 | TDbQuerySSize dbQuerySize = length(value(dbFinder.query).text); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:506:31: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 506 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:65: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 324 | TNames_Sliced names_sliced; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::pop(TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:925:24: required from ‘void seqan::Pool::pop(TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 925 | reader->pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1159:15: required from ‘void seqan::pop(Pool&, TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1159 | me.pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:926:18: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 926 | Ref_ = *cur; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:497:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 497 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:497:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 497 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:106: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 341 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 352 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TSpec = Namer<_skew7NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h: In instantiation of ‘TResult seqan::_skew7NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:426:13: required from ‘void seqan::Pipe, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 426 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe > >, Source<> >, Caster >; unsigned int m = 7; TPack = Tag; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:438:24: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:426:13: required from ‘void seqan::Pipe, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 426 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe > >, Source<> >, Caster >; unsigned int m = 7; TPack = Tag; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:438:24: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:335:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapLinear >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 148 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 247 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 259 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = int; TValue = unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:124:27: required from ‘bool seqan::CompareSkewDCStream::operator()(const seqan::SkewDCStream&, const seqan::SkewDCStream&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 124 | if (a.i.i3[i] < b.i.i3[i]) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:307:23: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 307 | if (!streamGreater(inValue[stream],inValue[rank[right]])) break; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: required from ‘seqan::Pipe, seqan::Merger7>& seqan::Pipe, seqan::Merger7>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 319 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:440:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 440 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_counter.h:105:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >, seqan::Skew7>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 105 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:620:9: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:520:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 520 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:537:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:454:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 454 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew3NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TSpec = Namer<_skew3NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h: In instantiation of ‘TResult seqan::_skew3NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapSliced >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TFunctor = seqan::filterI2 >, unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_lss.h:415:29: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:241:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapLinear >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 86 | o2.i2[0] = (*nameIn).i2; ++nameIn; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:301:6: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 301 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapSliced >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 3; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 3, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = unsigned int; unsigned int SIZE = 4; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 1; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 1, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = unsigned int; unsigned int SIZE = 5; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 2; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 2, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:328:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 328 | execute(searcher); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/search.cpp:513:39: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 513 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:142:117: warning: this statement may fall through [-Wimplicit-fallthrough=] 142 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:144:9: note: here 144 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:145:118: warning: this statement may fall through [-Wimplicit-fallthrough=] 145 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:147:9: note: here 147 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:149:103: warning: this statement may fall through [-Wimplicit-fallthrough=] 149 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:151:9: note: here 151 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:152:119: warning: this statement may fall through [-Wimplicit-fallthrough=] 152 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:154:9: note: here 154 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:156:105: warning: this statement may fall through [-Wimplicit-fallthrough=] 156 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:158:9: note: here 158 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 4, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 4, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 5, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 5, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 4, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 4, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 5, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 5, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:279:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:289:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple, Tag > >; TLess = MergeStreamComparer, Tuple, Tag >, _skew3ExtendComp, Tuple, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew7NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew3NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple >, Tag >, _skew7NCompMulti >, Tuple >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple >, Tag >, _skew7NCompMulti >, Tuple >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, 7, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, 7, BitPacked<> >, Tag >, _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, 7, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, 7, BitPacked<> >, Tag >, _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 79%] Linking CXX executable ../../../bin/search cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/search.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/search.dir/search.cpp.o -o ../../../bin/search -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 79%] Built target search make -f extras/apps/searchjoin/CMakeFiles/join.dir/build.make extras/apps/searchjoin/CMakeFiles/join.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin/CMakeFiles/join.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/searchjoin/CMakeFiles/join.dir/build.make extras/apps/searchjoin/CMakeFiles/join.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 80%] Building CXX object extras/apps/searchjoin/CMakeFiles/join.dir/join.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/searchjoin/CMakeFiles/join.dir/join.cpp.o -MF CMakeFiles/join.dir/join.cpp.o.d -o CMakeFiles/join.dir/join.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:53: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:51: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:44: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:316:37: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: 316 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index_extras.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:44: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:277:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 277 | prepare(joiner, db); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:328:37: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 328 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:277:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 277 | prepare(joiner, db); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:350:37: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 350 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:277:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 277 | prepare(joiner, db); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:362:37: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 362 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:336:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 336 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:780:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 780 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:366:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:277:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 277 | prepare(joiner, db); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:902:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 902 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 86 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet, Alloc > >, Owner > >; TShape = Shape, UngappedShape<0> >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:316:37: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: 316 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:86:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:126: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:103:8: warning: implicitly-declared ‘constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)’ is deprecated [-Wdeprecated-copy] 103 | struct VertexSA : public VertexEsa | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:125: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:290:17: note: because ‘seqan::VertexEsa’ has user-provided ‘seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long unsigned int]’ 290 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: synthesized method ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ first required here 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TShape = Shape, UngappedShape<0> >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet, Alloc > >, Owner > >; TShape = Shape, UngappedShape<0> >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:328:37: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: 328 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TShape = Shape >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet > >, Owner > >; TShape = Shape >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:350:37: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 350 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h: In instantiation of ‘void seqan::_qgramFillSuffixArray(TSA&, const StringSet&, TShape, TDir&, TBucketMap&, TStepSize, TWithConstraints) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TShape = Shape >; TDir = String >; TBucketMap = Nothing; TStepSize = unsigned int; TWithConstraints = False]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1639:24: required from ‘void seqan::createQGramIndex(TSA&, TDir&, TBucketMap&, const TText&, TShape&, TStepSize) [with TSA = String >, Alloc<> >; TDir = String >; TBucketMap = Nothing; TText = StringSet > >, Owner > >; TShape = Shape >; TStepSize = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1639 | _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:804:21: required from ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 804 | createQGramIndex(sa, dir, nothing, text, shape, stepSize); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:347:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 347 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:262:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 262 | index(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:362:37: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 362 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Exact()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1448:87: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1448 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1450:98: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1450 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // first hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1458:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1458 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1460:110: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1460 | sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos; // next hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1480:95: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1480 | if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos; // if bucket is enabled | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1482:106: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1482 | sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos; // hash | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:292:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 292 | _historyClear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2147:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2147 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_iterator.h:65, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:47: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:783:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 783 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:309:29: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 309 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:93, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘bool seqan::_moveIteratorsRight(Finder2, Index, Backtracking, TSpec> >&, const StageExact_&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:587:28: required from ‘bool seqan::_nextState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 587 | if (_moveIteratorsRight(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1277:38: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1277 | while (_nextState(finder, TStage())); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1254:14: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1254 | _find(finder, delegate, StageExact_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index_extras.h:65: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: synthesized method ‘seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >& seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >::operator=(const seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >&)’ first required here 651 | back(finder.textStack) = finder.textStack[length(finder.textStack) - 2]; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘bool seqan::_moveIteratorsRight(Finder2, Index, Backtracking, TSpec> >&, const StageExact_&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TSpec = Tag]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:587:28: required from ‘bool seqan::_nextState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 587 | if (_moveIteratorsRight(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1277:38: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageExact_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1277 | while (_nextState(finder, TStage())); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1254:14: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1254 | _find(finder, delegate, StageExact_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:244:15: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 244 | class Iter< TIndex, VSTree< TopDown > > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: synthesized method ‘seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >& seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >::operator=(const seqan::Iter, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >&)’ first required here 651 | back(finder.textStack) = finder.textStack[length(finder.textStack) - 2]; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:47: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:783:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 783 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:343:29: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: 343 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:651:32: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:147:15: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 147 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2751:9: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2751 | _clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:293:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 293 | clear(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:266:10: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 266 | goRoot(*this); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2745:27: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2745 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:783:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 783 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:309:29: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 309 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:783:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 783 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:343:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 343 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 541 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 138 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:138:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:360:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 360 | _historyPush(it); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:2296:14: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 2296 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:432:27: required from ‘bool seqan::_pushState(Finder2, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/find_backtracking_exp.h:1271:31: required from ‘void seqan::_find(Finder2, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1271 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:603:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 603 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:619:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 619 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 122 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:92: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:783:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 783 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:309:29: required from here /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: 309 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:122:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/iterator_adaptor.h:139:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 139 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:541:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 541 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:624:25: required from ‘typename seqan::Iterator >::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 624 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_myers_ukkonen.h:1634:63: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 1634 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:783:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 783 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:343:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 343 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_base.h:470:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 470 | return me; | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 197 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/segment_infix.h:197:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:98: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >, Owner > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc >; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1367:67: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc > >, Owner > >; TValue = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:461:16: required from ‘bool _parseText(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 461 | appendValue(parser.db.text, parser._text); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:394:50: required from ‘bool parseLine(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 394 | return _parseId(parser, reader) && _parseText(parser, reader); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:534:23: required from ‘bool load(Db&, const TFileName&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 534 | if (!parseLine(parser, reader)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:231:14: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 231 | if (!load(db, options.databaseFile)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:309:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 309 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(Pipe&, TValue&) [with TInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Skew7>; TSpec = Counter; TValue = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Skew7>, Counter>; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:386:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 386 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 387 | renamer, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 388 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:619:14: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 619 | Ref_ = *me; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 856 | arrayClearSpace(seq_array + start, old_length - start, removed_size, size); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc > >, Owner > >; TValue = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:461:16: required from ‘bool _parseText(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 461 | appendValue(parser.db.text, parser._text); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:394:50: required from ‘bool parseLine(DbParser&, TReader&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = void; TReader = seqan::RecordReader, seqan::SinglePass >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 394 | return _parseId(parser, reader) && _parseText(parser, reader); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/db.h:534:23: required from ‘bool load(Db&, const TFileName&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 534 | if (!parseLine(parser, reader)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:231:14: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 231 | if (!load(db, options.databaseFile)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:309:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 309 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc >; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc >; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:735:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Db, Alloc > >, Owner > >, void>; TValue2 = Db, Alloc > >, Owner > >, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 735 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Db, Alloc > >, Owner > >, void>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Db, Alloc > >, Owner > >, void>; typename Reference > >::Type = Db, Alloc > >, Owner > >, void>&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:778:40: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 778 | TDbSSize dbQuerySize = length(value(dbFinder.query).text); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Nothing; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:309:29: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 309 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:65: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 324 | TNames_Sliced names_sliced; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::pop(TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:925:24: required from ‘void seqan::Pool::pop(TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 925 | reader->pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1159:15: required from ‘void seqan::pop(Pool&, TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1159 | me.pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:926:18: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 926 | Ref_ = *cur; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:497:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 497 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:497:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 497 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: ‘struct seqan::Pair >’ declared here 97 | struct Pair > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:97:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:106: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 341 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 352 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple >, seqan::Tag >& seqan::Pair >, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew7NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TSpec = Namer<_skew7NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h: In instantiation of ‘TResult seqan::_skew7NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > >; TSource = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:426:13: required from ‘void seqan::Pipe, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 426 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe > >, Source<> >, Caster >; unsigned int m = 7; TPack = Tag; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:438:24: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:426:13: required from ‘void seqan::Pipe, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 426 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe > >, Source<> >, Caster >; unsigned int m = 7; TPack = Tag; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe > >, Source<> >, Caster >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple >, Tag >; TSpec = SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > >; TSource = Pipe > >, Source<> >, Caster >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:438:24: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned char; unsigned int BITSIZE1 = 24; unsigned int BITSIZE2 = 8]’ 112 | inline Pair(Pair const & _p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:335:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_bit_compressed.h:112:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapLinear >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 148 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 247 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 259 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = int; TValue = unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:124:27: required from ‘bool seqan::CompareSkewDCStream::operator()(const seqan::SkewDCStream&, const seqan::SkewDCStream&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 124 | if (a.i.i3[i] < b.i.i3[i]) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:307:23: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 307 | if (!streamGreater(inValue[stream],inValue[rank[right]])) break; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: required from ‘seqan::Pipe, seqan::Merger7>& seqan::Pipe, seqan::Merger7>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 319 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:440:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 440 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_counter.h:105:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >, seqan::Skew7>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 105 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:620:9: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:332:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:354:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 354 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:366:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 366 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TCompare = _skew3NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >; TSpec = Namer<_skew3NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h: In instantiation of ‘TResult seqan::_skew3NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapSliced >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TFunctor = seqan::filterI2 >, unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_lss.h:415:29: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, unsigned int, File > > >; TSource = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:241:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapLinear >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 86 | o2.i2[0] = (*nameIn).i2; ++nameIn; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:301:6: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 301 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapSliced >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = unsigned int; T2 = unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 3; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 3, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 3, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = unsigned int; unsigned int SIZE = 4; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 1; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 1, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = unsigned int; unsigned int SIZE = 5; typename seqan::StoredTupleValue_::Type = unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 2; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:50:21: required from ‘bool seqan::MergeStreamComparer::operator()(const seqan::PageBucket&, const seqan::PageBucket&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; Compare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 2, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 50 | return C(static_cast(*(a.cur)), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 | static_cast(*(b.cur))) > 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:356:13: required from ‘void seqan::_adjustHeapTowardLeaves(PriorityType&, TValue, TSize, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >; TSize = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 356 | if ( less ( element, me.heap[i] ) ) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:335:26: required from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 335 | _adjustHeapTowardLeaves(me, element, 0, 2 ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18: required from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 311 | ::seqan::pop(pqueue); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/include/seqan/index/index_sa_stree.h:177:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 177 | indexRequire(index, EsaSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_stree.h:265:33: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 265 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/finder.h:597:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 597 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:284:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 284 | execute(joiner); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin/join.cpp:320:41: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 320 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:142:117: warning: this statement may fall through [-Wimplicit-fallthrough=] 142 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:144:9: note: here 144 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:145:118: warning: this statement may fall through [-Wimplicit-fallthrough=] 145 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:147:9: note: here 147 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:149:103: warning: this statement may fall through [-Wimplicit-fallthrough=] 149 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:151:9: note: here 151 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:152:119: warning: this statement may fall through [-Wimplicit-fallthrough=] 152 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:154:9: note: here 154 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:156:105: warning: this statement may fall through [-Wimplicit-fallthrough=] 156 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:158:9: note: here 158 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter, Alloc > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String, Alloc > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String > >, seqan::Owner > >, seqan::IndexSa > >, seqan::VSTree > > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Iter > >, Owner > >, IndexSa > >, VSTree > > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘void seqan::eraseBack(T&) [with T = String > >, Owner > >, IndexSa > >, VSTree > > >, Alloc<> >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 4, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 4, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 5, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 5, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 4, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 4, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 4, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple, 5, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple, 5, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple, 5, BitPacked<> >, Tag >, _skew7ExtendComp >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:423:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple, Tuple >, Tag >, _skew7ExtendComp >, Tuple, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:432:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 1, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:279:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple >, Tag > >; TLess = MergeStreamComparer, Tuple >, Tag >, _skew7ExtendComp, Tuple >, Tag >, 2, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:289:6: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In member function ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Tuple, Tag > >, Alloc<> >; TValue = PageBucketExtended, Tuple, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Tuple, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended, Tuple, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended, Tuple, Tag > >; TLess = MergeStreamComparer, Tuple, Tag >, _skew3ExtendComp, Tuple, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TPoolSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew7NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tag > >; TLess = MergeStreamComparer >, Tag >, _skew3NComp >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple >, Tag >, _skew7NCompMulti >, Tuple >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple >, Tag > >; TLess = MergeStreamComparer >, Tuple >, Tag >, _skew7NCompMulti >, Tuple >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple >, Tag >, SorterSpec >, Tuple >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, 7, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, 7, BitPacked<> >, Tag >, _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String >, Tuple, 7, BitPacked<> >, Tag > >, Alloc<> >; TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1821:1, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag > >, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘void seqan::pop(PriorityType&) [with TValue = PageBucketExtended >, Tuple, 7, BitPacked<> >, Tag > >; TLess = MergeStreamComparer >, Tuple, 7, BitPacked<> >, Tag >, _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/priority_type_heap.h:333:8, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TPoolSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:311:18, inlined from ‘void seqan::Handler, seqan::Tag >::pop() [with THandler1 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::AdapterSpec>; THandler2 = seqan::Handler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:664:24, inlined from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:140:13, inlined from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, unsigned int, seqan::Tag >, seqan::String >, unsigned int, seqan::Pair > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13, inlined from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42, inlined from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1385:17, inlined from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, unsigned int>, unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, unsigned int, Tag >, String >, unsigned int, Pair > > > >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22, inlined from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/new: In function ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 80%] Linking CXX executable ../../../bin/join cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/join.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/join.dir/join.cpp.o -o ../../../bin/join -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 80%] Built target join make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 82%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/test_demultiplex.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/test_demultiplex.cpp.o -MF CMakeFiles/test_sflex_demultiplex.dir/test_demultiplex.cpp.o.d -o CMakeFiles/test_sflex_demultiplex.dir/test_demultiplex.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:46: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/score.h:42, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:50: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find.h:43: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index > >, IndexEsa<> >; TSource = Index > >, IndexEsa<> >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index > >, IndexEsa<> >; TSource = Index > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index > >, seqan::IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:67:8: required from ‘void findAllExactIndex(seqan::String&, const TPrefices&, const TFinder&, TStats&) [with TPrefices = seqan::StringSet > >; TFinder = seqan::Finder > >, seqan::IndexEsa<> > >; TStats = DemultiplexStats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 67 | class Finder< Index, TSpecFinder > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:322:22: required from ‘void SEQAN_TEST_findAllExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 322 | findAllExactIndex(res, readPieces, esaFinder, demultiplexStats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:552:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index > >, seqan::IndexEsa<> >& seqan::Index > >, seqan::IndexEsa<> >::operator=(const seqan::Index > >, seqan::IndexEsa<> >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:125: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: because ‘seqan::Index > >, seqan::IndexEsa<> >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]’ 548 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> > >, IndexEsa<> >; TSource = Index, Alloc<> > >, IndexEsa<> >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> > >, IndexEsa<> >; TSource = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:67:8: required from ‘void findAllExactIndex(seqan::String&, const TPrefices&, const TFinder&, TStats&) [with TPrefices = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TStats = DemultiplexStats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 67 | class Finder< Index, TSpecFinder > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:458:19: required from ‘void doAll(seqan::StringSet >&, TMultiplex&, TBarcodes&, TFinder&, DemultiplexStats&, bool) [with TBarcodes = seqan::StringSet, seqan::Alloc<> > >; TMultiplex = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 458 | findAllExactIndex(matches, multiplex, esaFinder, stats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:501:10: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 501 | doAll(res, multiplex, barcodes, esaFinder, demultiplexStats, false); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >& seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >::operator=(const seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: because ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]’ 548 | Index(Index const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:177:13: required from ‘void SEQAN_TEST_buildVariations_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 177 | Dna5String barcode = "ACTNG"; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:549:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:116: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h: In instantiation of ‘void seqan::posLocalize(TResult&, const Pair&, const String&) [with TResult = Pair >; TSize = long unsigned int; TSpec = Alloc<>; T1 = long unsigned int; T2 = long unsigned int; TPack = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:768:16: required from ‘typename seqan::Suffix::Type seqan::suffix(const StringSet&, const TPosition&) [with TString = String >; TSpec = Owner<>; TPosition = Pair >; typename Suffix::Type = Segment >, SuffixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 768 | posLocalize(lPos, pos, stringSetLimits(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:803:25: required from ‘seqan::Pair >::Type> seqan::_equalRangeSA(TText&, SearchTreeIterator, TQuery&, typename Difference::Type) [with TText = const StringSet > >; TSA = const String >, Alloc<> >; TSpec = SortedList; TQuery = const String >; typename Iterator >::Type = const Pair >*; typename Difference::Type = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 803 | TSuffix suf = suffix(text, *treeIter); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:897:23: required from ‘seqan::Pair >::Type> seqan::equalRangeSAIterator(const TText&, const TSA&, const TQuery&) [with TText = StringSet > >; TSA = String >, Alloc<> >; TQuery = String >; typename Iterator >::Type = const Pair >*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 897 | return _equalRangeSA(text, SearchTreeIterator(sa), query); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1930:38: required from ‘void seqan::_findFirstIndex(Finder, TSpecFinder>&, const TPattern&, EsaFindMlr) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >; EsaFindMlr = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1930 | finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:292:19: required from ‘bool seqan::find(Finder, TSpecFinder>&, const TPattern&) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 292 | _findFirstIndex(finder, needle(pattern), TSpecFinder()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:274:10: required from ‘int findExactIndex(const TPrefix&, TFinder&) [with TPrefix = seqan::String >; TFinder = seqan::Finder > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | if (find(finder, prefix)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:290:27: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 290 | int res = findExactIndex(readPieces[i], esaFinder); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:699:12: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 699 | result = pos; | ~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:653:49: required from ‘int seqan::SequenceStreamImpl_::readBatch(seqan::StringSet&, seqan::StringSet&, unsigned int, const TFormatTag&) [with TId = seqan::String >; TIdSpec = seqan::Owner<>; TSequence = seqan::String >; TSeqSpec = seqan::Owner<>; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 653 | if ((res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag)) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:819:37: required from ‘int seqan::readBatch(StringSet&, StringSet&, SequenceStream&, unsigned int) [with TId = String >; TIdSpec = Owner<>; TSequence = String >; TSeqSpec = Owner<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 819 | res = seqIO._impl->readBatch(ids, seqs, num, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:72:15: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 72 | if (readBatch(ids, seqs, seqStream, records) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:823:49: required from ‘int seqan::SequenceStreamImpl_::readAll(seqan::StringSet&, seqan::StringSet&, const TFormatTag&) [with TId = seqan::String >; TIdSpec = seqan::Owner<>; TSequence = seqan::String, seqan::Alloc<> >; TSeqSpec = seqan::Owner<>; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 823 | if ((res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag)) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:940:35: required from ‘int seqan::readAll(StringSet&, StringSet&, SequenceStream&) [with TId = String >; TIdSpec = Owner<>; TSequence = String, Alloc<> >; TSeqSpec = Owner<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 940 | res = seqIO._impl->readAll(ids, seqs, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:90:13: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 90 | if (readAll(bcids, bcs, bcStream) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:98: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index > >, IndexEsa<> >; TSource = Index > >, IndexEsa<> >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index > >, IndexEsa<> >; TValue2 = Index > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index > >, IndexEsa<> >; typename Reference > >::Type = Index > >, IndexEsa<> >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:118:15: required from ‘typename seqan::Parameter_ >::Type seqan::container(Finder, TSpecFinder>&) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; typename Parameter_ >::Type = Index > >, IndexEsa<> >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 118 | return value(me.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:1165:18: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = Finder > >, IndexEsa<> > >; typename Parameter_::Type>::Type = Index > >, IndexEsa<> >&; typename Haystack::Type = Index > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1165 | return container(obj); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1928:40: required from ‘void seqan::_findFirstIndex(Finder, TSpecFinder>&, const TPattern&, EsaFindMlr) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >; EsaFindMlr = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1928 | Index &index = haystack(finder); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:292:19: required from ‘bool seqan::find(Finder, TSpecFinder>&, const TPattern&) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 292 | _findFirstIndex(finder, needle(pattern), TSpecFinder()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:274:10: required from ‘int findExactIndex(const TPrefix&, TFinder&) [with TPrefix = seqan::String >; TFinder = seqan::Finder > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 274 | if (find(finder, prefix)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:290:27: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 290 | int res = findExactIndex(readPieces[i], esaFinder); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index > >, seqan::IndexEsa<> >& seqan::Index > >, seqan::IndexEsa<> >::operator=(const seqan::Index > >, seqan::IndexEsa<> >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: because ‘seqan::Index > >, seqan::IndexEsa<> >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]’ 548 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(Pipe&, TValue&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>; TSpec = Counter; TValue = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>, Counter>; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:386:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 386 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 387 | renamer, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 388 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:619:14: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 619 | Ref_ = *me; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = int; TEndPosition = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:355:9: required from ‘void clipBarcodes(TSeqs&, const seqan::String&, unsigned int) [with TSeqs = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 355 | erase(seqs[i], 0 , len); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:344:14: required from ‘void SEQAN_TEST_clipBarcodes_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 344 | clipBarcodes(seqs, matches, 6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:553:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = int; TEndPosition = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:355:9: required from ‘void clipBarcodes(TSeqs&, const seqan::String&, unsigned int) [with TSeqs = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 355 | erase(seqs[i], 0 , len); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:344:14: required from ‘void SEQAN_TEST_clipBarcodes_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 344 | clipBarcodes(seqs, matches, 6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:553:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> > >, IndexEsa<> >; TSource = Index, Alloc<> > >, IndexEsa<> >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> > >, IndexEsa<> >; TValue2 = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> > >, IndexEsa<> >; typename Reference > >::Type = Index, Alloc<> > >, IndexEsa<> >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:118:15: required from ‘typename seqan::Parameter_ >::Type seqan::container(Finder, TSpecFinder>&) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; typename Parameter_ >::Type = Index, Alloc<> > >, IndexEsa<> >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 118 | return value(me.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:1165:18: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:292:19: required from ‘bool seqan::find(Finder, TSpecFinder>&, const TPattern&) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 292 | _findFirstIndex(finder, needle(pattern), TSpecFinder()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:274:10: required from ‘int findExactIndex(const TPrefix&, TFinder&) [with TPrefix = seqan::String >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | if (find(finder, prefix)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:326:33: required from ‘void findAllExactIndex(seqan::String&, const TPrefices&, const TFinder&, TStats&) [with TPrefices = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TStats = DemultiplexStats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 326 | int hit = findExactIndex(prefices[i], finderSet[tid]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:458:19: required from ‘void doAll(seqan::StringSet >&, TMultiplex&, TBarcodes&, TFinder&, DemultiplexStats&, bool) [with TBarcodes = seqan::StringSet, seqan::Alloc<> > >; TMultiplex = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 458 | findAllExactIndex(matches, multiplex, esaFinder, stats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:501:10: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 501 | doAll(res, multiplex, barcodes, esaFinder, demultiplexStats, false); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >& seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >::operator=(const seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: because ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]’ 548 | Index(Index const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:65: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:497:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 497 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 324 | TNames_Sliced names_sliced; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::pop(TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:925:24: required from ‘void seqan::Pool::pop(TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 925 | reader->pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1159:15: required from ‘void seqan::pop(Pool&, TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1159 | me.pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:926:18: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 926 | Ref_ = *cur; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, Tag >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, Tag >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, Tag >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, Tag >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::Tag >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::Tag >; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:376:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 376 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, long unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::Tag >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, Tag >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, Tag >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, long unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::Tag >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, Tag >, Tag >, SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, Tag >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::Tag >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:106: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 341 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 352 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:418:11: required from ‘void seqan::Pipe, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 418 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = Tag; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:426:13: required from ‘void seqan::Pipe, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 426 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = Tag; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, Tag >, Tag >; TSpec = SorterSpec >, Tuple, 7, Tag >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:438:24: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 438 | tmpRef->i1 = localPos; | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew7NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h: In instantiation of ‘TResult seqan::_skew7NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:335:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 148 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 247 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 259 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:124:27: required from ‘bool seqan::CompareSkewDCStream::operator()(const seqan::SkewDCStream&, const seqan::SkewDCStream&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 124 | if (a.i.i3[i] < b.i.i3[i]) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:307:23: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 307 | if (!streamGreater(inValue[stream],inValue[rank[right]])) break; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: required from ‘seqan::Pipe, seqan::Merger7>& seqan::Pipe, seqan::Merger7>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 319 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:440:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 440 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_counter.h:105:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >, seqan::Skew7>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 105 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:620:9: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, Tag >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:498:14: required from ‘void SEQAN_TEST_doAll_Exact_Multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 498 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:557:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew3NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew3NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h: In instantiation of ‘TResult seqan::_skew3NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TFunctor = seqan::filterI2 >, long unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_lss.h:415:29: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:241:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 86 | o2.i2[0] = (*nameIn).i2; ++nameIn; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:301:6: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 301 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:329:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 3; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:68:21: required from ‘bool seqan::AdaptorCompare2Less::operator()(const typename TCompare::first_argument_type&, const typename TCompare::second_argument_type&) const [with TCompare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 3, int>; typename TCompare::first_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >; typename TCompare::second_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 68 | return C(a, b) < 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~^~~~~~ /usr/include/c++/14/bits/predefined_ops.h:158:30: required from ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Iterator2 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = seqan::AdaptorCompare2Less, seqan::Tuple >, seqan::Tag >, 3, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 158 | { return bool(_M_comp(*__it1, *__it2)); } /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1771:14: required from ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 3, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1771 | if (__comp(__i, __first)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1811:25: required from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 3, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1811 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1902:31: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 4; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 1; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:68:21: required from ‘bool seqan::AdaptorCompare2Less::operator()(const typename TCompare::first_argument_type&, const typename TCompare::second_argument_type&) const [with TCompare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 1, int>; typename TCompare::first_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >; typename TCompare::second_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 68 | return C(a, b) < 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~ /usr/include/c++/14/bits/predefined_ops.h:158:30: required from ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Iterator2 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = seqan::AdaptorCompare2Less, seqan::Tuple >, seqan::Tag >, 1, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 158 | { return bool(_M_comp(*__it1, *__it2)); } /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1771:14: required from ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 1, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1771 | if (__comp(__i, __first)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1811:25: required from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 1, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1811 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1902:31: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 5; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 2; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:68:21: required from ‘bool seqan::AdaptorCompare2Less::operator()(const typename TCompare::first_argument_type&, const typename TCompare::second_argument_type&) const [with TCompare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 2, int>; typename TCompare::first_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >; typename TCompare::second_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 68 | return C(a, b) < 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~ /usr/include/c++/14/bits/predefined_ops.h:158:30: required from ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Iterator2 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = seqan::AdaptorCompare2Less, seqan::Tuple >, seqan::Tag >, 2, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 158 | { return bool(_M_comp(*__it1, *__it2)); } /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1771:14: required from ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 2, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1771 | if (__comp(__i, __first)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1811:25: required from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 2, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1811 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1902:31: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:284:14: required from ‘void SEQAN_TEST_findExactIndex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 284 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_demultiplex.cpp:551:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:142:117: warning: this statement may fall through [-Wimplicit-fallthrough=] 142 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:144:9: note: here 144 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:145:118: warning: this statement may fall through [-Wimplicit-fallthrough=] 145 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:147:9: note: here 147 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:149:103: warning: this statement may fall through [-Wimplicit-fallthrough=] 149 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:151:9: note: here 151 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:152:119: warning: this statement may fall through [-Wimplicit-fallthrough=] 152 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:154:9: note: here 154 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:156:105: warning: this statement may fall through [-Wimplicit-fallthrough=] 156 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:158:9: note: here 158 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 6, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 4, Tag >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, Tag >, Tag >, SorterSpec >, Tuple, Tuple, 5, Tag >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, Tag >, Tag >, MapperSpec >, Tuple, Tuple, 6, Tag >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h: In static member function ‘static const char* seqan::ClassTest::StaticData::_computePathToRoot()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:694:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated copying between 0 and 73 bytes from a string of length 78 [-Wstringop-truncation] 694 | strncpy(&buffer[0], file, pos); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 82%] Linking CXX executable ../../../bin/test_sflex_demultiplex cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sflex_demultiplex.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/test_sflex_demultiplex.dir/test_demultiplex.cpp.o -o ../../../bin/test_sflex_demultiplex -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 82%] Built target test_sflex_demultiplex make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 82%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/test_trimming.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/test_trimming.cpp.o -MF CMakeFiles/test_sflex_trimming.dir/test_trimming.cpp.o.d -o CMakeFiles/test_sflex_trimming.dir/test_trimming.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:48: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:46: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:501:40: required from ‘int seqan::SequenceStreamImpl_::readRecord(TId&, TSequence&, const TFormatTag&) [with TId = seqan::String >; TSequence = seqan::String >; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 501 | res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:697:38: required from ‘int seqan::readRecord(TId&, TSequence&, SequenceStream&) [with TId = String >; TSequence = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 697 | res = seqIO._impl->readRecord(id, seq, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:150:24: required from ‘void SEQAN_TEST_sliding_window_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 150 | if (seqan::readRecord(id, seq, inStream) == 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:218:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = unsigned int; TEndPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/read_trimming.h:219:7: required from ‘unsigned int trimRead(TSeq&, unsigned int, const TSpec&) [with TSeq = seqan::String >; TSpec = Mean]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 219 | erase(seq, cut_pos, length(seq)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:153:27: required from ‘void SEQAN_TEST_sliding_window_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 153 | unsigned res = trimRead(seq, 20, m); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:218:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = unsigned int; TEndPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/read_trimming.h:219:7: required from ‘unsigned int trimRead(TSeq&, unsigned int, const TSpec&) [with TSeq = seqan::String >; TSpec = Mean]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 219 | erase(seq, cut_pos, length(seq)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:153:27: required from ‘void SEQAN_TEST_sliding_window_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 153 | unsigned res = trimRead(seq, 20, m); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:218:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h: In static member function ‘static const char* seqan::ClassTest::StaticData::_computePathToRoot()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:694:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated copying between 0 and 73 bytes from a string of length 78 [-Wstringop-truncation] 694 | strncpy(&buffer[0], file, pos); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In static member function ‘static const char* seqan::ClassTest::StaticData::_computePathToRoot()’, inlined from ‘static const char* seqan::ClassTest::StaticData::pathToRoot()’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:705:40, inlined from ‘void SEQAN_TEST_cut_tail_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:165:32: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:694:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated copying between 0 and 73 bytes from a string of length 78 [-Wstringop-truncation] 694 | strncpy(&buffer[0], file, pos); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static const char* seqan::ClassTest::StaticData::_computePathToRoot()’, inlined from ‘static const char* seqan::ClassTest::StaticData::pathToRoot()’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:705:40, inlined from ‘void SEQAN_TEST_cut_bwa_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ at /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_trimming.cpp:190:32: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:694:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated copying between 0 and 73 bytes from a string of length 78 [-Wstringop-truncation] 694 | strncpy(&buffer[0], file, pos); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Linking CXX executable ../../../bin/test_sflex_trimming cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sflex_trimming.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/test_sflex_trimming.dir/test_trimming.cpp.o -o ../../../bin/test_sflex_trimming -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 83%] Built target test_sflex_trimming make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 85%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/test_adapter.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/test_adapter.cpp.o -MF CMakeFiles/test_sflex_adapter.dir/test_adapter.cpp.o.d -o CMakeFiles/test_sflex_adapter.dir/test_adapter.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:49: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:47: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:51: /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h: In instantiation of ‘unsigned int stripPair(TSeq&, TSeq&) [with TSeq = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:224:29: required from ‘void SEQAN_TEST_strip_pair_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 224 | unsigned insert = stripPair(seq1,seq2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:245:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:297:16: warning: implicitly-declared ‘seqan::Align > >::Align(const seqan::Align > >&)’ is deprecated [-Wdeprecated-copy] 297 | TAlign align = ret.i2; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:89: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:59:15: required from ‘void SEQAN_TEST_get_overlap_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 59 | TSequence seq1 = "AAAAAAAAA"; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:239:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = long unsigned int; TEndPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = long unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = long unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:538:15: required from ‘unsigned int stripAdapter(TSeq&, TAdapter&, const TSpec&) [with TSeq = seqan::String >; TAdapter = seqan::String, seqan::Alloc<> >; TSpec = Auto]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 538 | seqan::erase(seq, length(seq) - overlap, length(seq)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:198:28: required from ‘void SEQAN_TEST_strip_adapter_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 198 | int removed = stripAdapter(seq, ada, Auto()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:243:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = long unsigned int; TEndPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = long unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = long unsigned int; TEndPosition = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:538:15: required from ‘unsigned int stripAdapter(TSeq&, TAdapter&, const TSpec&) [with TSeq = seqan::String >; TAdapter = seqan::String, seqan::Alloc<> >; TSpec = Auto]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 538 | seqan::erase(seq, length(seq) - overlap, length(seq)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:198:28: required from ‘void SEQAN_TEST_strip_adapter_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 198 | int removed = stripAdapter(seq, ada, Auto()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:243:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = String >; typename Reference > >::Type = String >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gaps_array.h:368:17: required from ‘typename seqan::Source > >::Type& seqan::source(Gaps >&) [with TSequence = String >; typename Source > >::Type = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 368 | return value(gaps._source); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:230:22: required from ‘unsigned int getOverlap(TAlign&) [with TAlign = seqan::Align > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 230 | return length(source(row1)) - countTotalGaps(row2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:533:26: required from ‘unsigned int stripAdapter(TSeq&, TAdapter&, const TSpec&) [with TSeq = seqan::String >; TAdapter = seqan::String, seqan::Alloc<> >; TSpec = Auto]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 533 | int overlap = getOverlap(ret.i2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:198:28: required from ‘void SEQAN_TEST_strip_adapter_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 198 | int removed = stripAdapter(seq, ada, Auto()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_adapter.cpp:243:2: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 85%] Linking CXX executable ../../../bin/test_sflex_adapter cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sflex_adapter.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/test_sflex_adapter.dir/test_adapter.cpp.o -o ../../../bin/test_sflex_adapter -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 85%] Built target test_sflex_adapter make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 85%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/test_general_processing.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/test_general_processing.cpp.o -MF CMakeFiles/test_sflex_general_processing.dir/test_general_processing.cpp.o.d -o CMakeFiles/test_sflex_general_processing.dir/test_general_processing.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/general_processing.h:54, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:52: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:47: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = int; TEndPosition = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 1048 | TSize_ ret_ = _clearSpace( /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~^ 1049 | me, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~ 1050 | static_cast(size), /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TSize = int; TBeginPosition = int; TEndPosition = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TBeginPosition = int; TEndPosition = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 2267 | resizeSpace(me, 0, pos, pos_end); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/general_processing.h:604:22: required from ‘void preTrim(TSeqs&, TIds&, unsigned int, unsigned int, unsigned int, GeneralStats&) [with TSeqs = seqan::StringSet, seqan::Alloc<> > >; TIds = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 604 | erase(seqs[i], 0, head); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:446:12: required from ‘void SEQAN_TEST_preTrim_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 446 | preTrim(seqs2, ids2, 3, 3, 4, stats); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:630:5: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 1960 | SEQAN_TEST_ ## test_name(); \ /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = int; TEndPosition = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TSize = int; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String, Alloc<> >; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/general_processing.h:604:22: required from ‘void preTrim(TSeqs&, TIds&, unsigned int, unsigned int, unsigned int, GeneralStats&) [with TSeqs = seqan::StringSet, seqan::Alloc<> > >; TIds = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 604 | erase(seqs[i], 0, head); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:446:12: required from ‘void SEQAN_TEST_preTrim_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 446 | preTrim(seqs2, ids2, 3, 3, 4, stats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:630:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TValue = const char [31]; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = String, Alloc<> >; TTargetSpec = Alloc<>; TValue = char [31]; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = String, Alloc<> >; TString2 = char [31]; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> > >; TValue = char [31]]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:59:16: required from ‘void SEQAN_TEST_findN_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 59 | appendValue(seqs, "ATGACTGTACACGTGATCGTACGTAGCAGC"); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:625:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const char [7]; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = String >; TTargetSpec = Alloc<>; TValue = char [7]; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = String >; TString2 = char [7]; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet > >; TValue = char [7]]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:335:16: required from ‘void SEQAN_TEST_processN_paired_multiplex_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 335 | appendValue(multiplex, "ACTGTA"); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:629:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1481:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&) [with T = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TValue = const char [11]; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1481 | valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1500:54: required from ‘void seqan::appendValue(String&, const TValue&, Tag) [with TTargetValue = String, Alloc<> >; TTargetSpec = Alloc<>; TValue = char [11]; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1500 | AppendValueToString_ >::appendValue_(me, _value); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_owner.h:146:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = String, Alloc<> >; TString2 = char [11]; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 146 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:1718:16: required from ‘void seqan::appendValue(T&, const TValue&) [with T = StringSet, Alloc<> > >; TValue = char [11]]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1718 | appendValue(me, _value, typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:427:16: required from ‘void SEQAN_TEST_preTrim_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 427 | appendValue(seqs, "ACGTAACTGA"); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/test_general_processing.cpp:630:5: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1960 | SEQAN_TEST_ ## test_name(); \ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ [ 87%] Linking CXX executable ../../../bin/test_sflex_general_processing cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sflex_general_processing.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/test_sflex_general_processing.dir/test_general_processing.cpp.o -o ../../../bin/test_sflex_general_processing -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 87%] Built target test_sflex_general_processing make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 87%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/seqan_flexlib.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/seqan_flexlib.cpp.o -MF CMakeFiles/seqan_flexlib.dir/seqan_flexlib.cpp.o.d -o CMakeFiles/seqan_flexlib.dir/seqan_flexlib.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:53: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:54, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/fai_index.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:83: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:166: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:174: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:60: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:485:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 485 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:495:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 495 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:505:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 505 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:515:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 515 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:525:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 525 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_align.h:535:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 535 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:62: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2357:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2357 | if (alignQualityStoreLengthPre == 0u) | ^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store/store_all.h:2361:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2361 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:40, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:52, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:72: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:45:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:54:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:63:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:401:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 401 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:507:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 507 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:42:48: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public ::std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:57:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public ::std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:257:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 257 | struct insertBucket : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:372:53: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 372 | struct insertBucket : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:45: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_set.h:373:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:70: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:404:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 404 | public::std::binary_function // functor for operator> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:744:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 744 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_base.h:760:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 760 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:80: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:854:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 854 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:902:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 902 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:970:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 970 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1039:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1039 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1073:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1073 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:1121:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1121 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2093:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2093 | struct _qgramComp : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_qgram.h:2112:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2112 | public ::std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:46:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_qsort.h:85:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public ::std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:96: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:99: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:110:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public ::std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:143:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public ::std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:100: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:103: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:141:29: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:109: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:59:42: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:164:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, KasaiOriginal)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:312:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 312 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:313:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 313 | LCP[isa - 1] = h; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const TText&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:379:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 379 | for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:380:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 380 | LCP[i] = h | mark; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h: In function ‘void seqan::_createLCPTableRandomAccess(TLCPTable&, const StringSet&, const TSA&, Kasai)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:483:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 483 | for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_lcp.h:484:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 484 | LCP[i] = h | mark; | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:113: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_bwt.h:144:50: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public ::std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:120: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:585:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 585 | public ::std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:128: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h: In function ‘void seqan::_storeWotdChildren(Index > >&, TSize, TSize)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:504:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 504 | } else | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_dfi.h:506:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 506 | for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:136: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/repeat_base.h:149:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 149 | struct RepeatLess_ : public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:157: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h: In function ‘typename seqan::Iterator >::Type seqan::_upperBoundLcpe(TText&, TSA&, SearchTreeIterator, TQuery&, TDiff_, TDiff_)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1498:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1498 | for(; i && ordEqual(*t, convert(*q)); --i, ++t, ++q) ; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1501:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1501 | if (q == qEnd || t == tEnd || !ordGreater(*t, convert(*q))) { | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp: In function ‘seqan::ArgumentParser initParser()’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:610:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 610 | std::auto_ptr argParseBuilder; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/test_system.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:62, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:54: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:71: /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h: In instantiation of ‘unsigned int stripPair(TSeq&, TSeq&) [with TSeq = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:411:12: required from ‘unsigned int stripPairBatch(seqan::StringSet >&, seqan::StringSet&, seqan::StringSet >&, seqan::StringSet&, AdapterTrimmingStats&, bool) [with TSeq = seqan::String >; TId = seqan::String >]’ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: 411 | stripPair(read1, read2); /usr/include/c++/14/bits/unique_ptr.h:59:28: note: | ~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1926:27: required from ‘void adapterTrimmingStage(AdapterTrimmingParams&, TSeqs&, TIds&, TSeqs&, TIds&, bool) [with TSeqs = seqan::String > > >; TIds = seqan::String > > >]’ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: 1926 | stripPairBatch(seqSet1[i], idSet1[i], seqSet2[i], idSet2[i], params.stats, tagOpt); /usr/include/c++/14/bits/unique_ptr.h:59:28: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2726:37: required from here /usr/include/c++/14/bits/unique_ptr.h:59:28: note: 2726 | adapterTrimmingStage(adapterTrimmingParams, seqSet1, idSet1, seqSet2, idSet2, tagOpt); /usr/include/c++/14/bits/unique_ptr.h:59:28: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/adapter_trimming.h:297:16: warning: implicitly-declared ‘seqan::Align >, seqan::Tag >::Align(const seqan::Align >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 297 | TAlign align = ret.i2; | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align.h:89: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: because ‘seqan::Align >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String >; TSpec = seqan::Tag]’ 131 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:69, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> > >, IndexEsa<> >; TSource = Index, Alloc<> > >, IndexEsa<> >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1020:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> > >, IndexEsa<> >; TSource = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1020 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:1065:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1065 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:170:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 170 | assign(*this, source_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:67:8: required from ‘void findAllExactIndex(seqan::String&, const TPrefices&, const TFinder&, TStats&) [with TPrefices = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TStats = DemultiplexStats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 67 | class Finder< Index, TSpecFinder > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:458:19: required from ‘void doAll(seqan::StringSet >&, TMultiplex&, TBarcodes&, TFinder&, DemultiplexStats&, bool) [with TBarcodes = seqan::StringSet, seqan::Alloc<> > >; TMultiplex = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 458 | findAllExactIndex(matches, multiplex, esaFinder, stats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1733:14: required from ‘int demultiplexingStage(DemultiplexingParams&, TSeqsVec&, TIdsVec&, TFinder&, TMap&, GeneralStats&) [with TSeqsVec = seqan::String > > >; TIdsVec = seqan::String > > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TMap = seqan::String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 1733 | doAll(groups, params.multiplex, params.barcodes, esaFinder, params.stats, params.exclude); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2659:40: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: 2659 | if (demultiplexingStage(demultiplexingParams, seqSet, idSet, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2660 | esaFinder, map, generalStats) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/align/align_base.h:131:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:142:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >& seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >::operator=(const seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >&)’ is deprecated [-Wdeprecated-copy] 142 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:125: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: because ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]’ 548 | Index(Index const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: required from ‘void seqan::operator<<(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 826 | assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:110:15: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 110 | suffixArray << creator; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:802:19: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 802 | *_cur = *src; | ~~~~~~^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:55, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:71: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index.h:98: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:347:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 347 | o1.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:357:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 357 | o0.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:361:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | o3.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:365:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 365 | o5.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:369:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 369 | o6.i1 = typename Value::Type, 1>::Type(); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:125: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:126: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:127: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:408:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:412:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:424:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:426:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:428:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:430:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:435:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:437:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:441:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:454:128: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:456:129: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:458:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:460:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:465:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:467:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:471:130: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p; | ~~~~~~^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:653:49: required from ‘int seqan::SequenceStreamImpl_::readBatch(seqan::StringSet&, seqan::StringSet&, unsigned int, const TFormatTag&) [with TId = seqan::String >; TIdSpec = seqan::Owner<>; TSequence = seqan::String >; TSeqSpec = seqan::Owner<>; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 653 | if ((res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag)) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:819:37: required from ‘int seqan::readBatch(StringSet&, StringSet&, SequenceStream&, unsigned int) [with TId = String >; TIdSpec = Owner<>; TSequence = String >; TSeqSpec = Owner<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 819 | res = seqIO._impl->readBatch(ids, seqs, num, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1225:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1225 | if (seqan::readBatch(ids, seqs, seqStream, records) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:262:12: required from ‘int seqan::_clearAndReserveMemory(TIdString&, TSeqString&, RecordReader >&, const TTag&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TSpec = Tag; TTag = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 262 | reserve(seq, seqLength, Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/read_fasta_fastq.h:557:37: required from ‘int seqan::readRecord(TIdString&, TSeqString&, RecordReader&, const Fasta&) [with TIdString = String >; TSeqString = String, Alloc<> >; TFile = String >; TPass = DoublePass >; Fasta = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 557 | int res = _clearAndReserveMemory(meta, seq, reader, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:823:49: required from ‘int seqan::SequenceStreamImpl_::readAll(seqan::StringSet&, seqan::StringSet&, const TFormatTag&) [with TId = seqan::String >; TIdSpec = seqan::Owner<>; TSequence = seqan::String, seqan::Alloc<> >; TSeqSpec = seqan::Owner<>; TFormatTag = seqan::Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 823 | if ((res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag)) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream.h:940:35: required from ‘int seqan::readAll(StringSet&, StringSet&, SequenceStream&) [with TId = String >; TIdSpec = Owner<>; TSequence = String, Alloc<> >; TSeqSpec = Owner<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 940 | res = seqIO._impl->readAll(ids, seqs, Fasta()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1254:23: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1254 | if (seqan::readAll(params.barcodeIds, params.barcodes, bcStream) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairIncrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:382:10: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 382 | setHost(p, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1032:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1032 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(Pipe&, TValue&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>; TSpec = Counter; TValue = Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Skew7>, Counter>; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:386:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 386 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 387 | renamer, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~ 388 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:108:13: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 108 | creator_t creator(unsigner, stringSetLimits(stringSet)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:619:14: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 619 | Ref_ = *me; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc<> >; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:58: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:116, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:55: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h: In instantiation of ‘void seqan::posLocalize(TResult&, const Pair&, const String&) [with TResult = Pair >; TSize = long unsigned int; TSpec = Alloc<>; T1 = long unsigned int; T2 = long unsigned int; TPack = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:768:16: required from ‘typename seqan::Suffix::Type seqan::suffix(const StringSet&, const TPosition&) [with TString = String, Alloc<> >; TSpec = Owner<>; TPosition = Pair >; typename Suffix::Type = Segment, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 768 | posLocalize(lPos, pos, stringSetLimits(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:803:25: required from ‘seqan::Pair >::Type> seqan::_equalRangeSA(TText&, SearchTreeIterator, TQuery&, typename Difference::Type) [with TText = const StringSet, Alloc<> > >; TSA = const String >, Alloc<> >; TSpec = SortedList; TQuery = const String >; typename Iterator >::Type = const Pair >*; typename Difference::Type = long int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 803 | TSuffix suf = suffix(text, *treeIter); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:897:23: required from ‘seqan::Pair >::Type> seqan::equalRangeSAIterator(const TText&, const TSA&, const TQuery&) [with TText = StringSet, Alloc<> > >; TSA = String >, Alloc<> >; TQuery = String >; typename Iterator >::Type = const Pair >*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 897 | return _equalRangeSA(text, SearchTreeIterator(sa), query); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index_esa.h:1930:38: required from ‘void seqan::_findFirstIndex(Finder, TSpecFinder>&, const TPattern&, EsaFindMlr) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >; EsaFindMlr = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1930 | finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:292:19: required from ‘bool seqan::find(Finder, TSpecFinder>&, const TPattern&) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 292 | _findFirstIndex(finder, needle(pattern), TSpecFinder()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:274:10: required from ‘int findExactIndex(const TPrefix&, TFinder&) [with TPrefix = seqan::String >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 274 | if (find(finder, prefix)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:326:33: required from ‘void findAllExactIndex(seqan::String&, const TPrefices&, const TFinder&, TStats&) [with TPrefices = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TStats = DemultiplexStats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 326 | int hit = findExactIndex(prefices[i], finderSet[tid]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:458:19: required from ‘void doAll(seqan::StringSet >&, TMultiplex&, TBarcodes&, TFinder&, DemultiplexStats&, bool) [with TBarcodes = seqan::StringSet, seqan::Alloc<> > >; TMultiplex = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 458 | findAllExactIndex(matches, multiplex, esaFinder, stats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1733:14: required from ‘int demultiplexingStage(DemultiplexingParams&, TSeqsVec&, TIdsVec&, TFinder&, TMap&, GeneralStats&) [with TSeqsVec = seqan::String > > >; TIdsVec = seqan::String > > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TMap = seqan::String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1733 | doAll(groups, params.multiplex, params.barcodes, esaFinder, params.stats, params.exclude); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2659:40: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2659 | if (demultiplexingStage(demultiplexingParams, seqSet, idSet, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2660 | esaFinder, map, generalStats) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_set_base.h:699:12: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 699 | result = pos; | ~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1610:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1610 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1444:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1444 | arrayMoveForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1465:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1465 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:849:31: required from ‘static typename seqan::Size::Type seqan::ClearSpaceExpandStringBase_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type) [with T = seqan::String >; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 849 | arrayConstructMove(old_array, old_array + start, seq_array); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1014:62: required from ‘typename seqan::Size >::Type seqan::_clearSpace(String&, TSize, TPosition, TPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1014 | return ClearSpaceStringBase_ >::_clearSpace_(me, size, pos_begin, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = int; TEndPosition = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/general_processing.h:716:22: required from ‘void preTrim(TSeqs&, TIds&, TMulti&, unsigned int, unsigned int, unsigned int, GeneralStats&) [with TSeqs = seqan::StringSet > >; TIds = seqan::StringSet > >; TMulti = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 716 | erase(seqs[i], 0, head); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1607:24: required from ‘void preprocessingStage(TSeqs&, TIds&, DemultiplexingParams&, ProcessingParams&, const seqan::ArgumentParser&, GeneralStats&) [with TSeqs = seqan::StringSet > >; TIds = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1607 | preTrim(seqs, ids, demultiplexingParams.multiplex, processingParams.trimLeft, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1608 | processingParams.trimRight, processingParams.minLen, generalStats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2655:35: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2655 | preprocessingStage(seqSet[0], idSet[0], demultiplexingParams, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2656 | processingParams, parser, generalStats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1589:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1589 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:65: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe >, TPair, TLimitsString> >& seqan::Pipe >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 317 | sorter << sampler; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:599:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 599 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 324 | TNames_Sliced names_sliced; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::pop(TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:925:24: required from ‘void seqan::Pool::pop(TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 925 | reader->pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1159:15: required from ‘void seqan::pop(Pool&, TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1159 | me.pop(Ref_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:62:7: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 62 | pop(in, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~^~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:926:18: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 926 | Ref_ = *cur; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:414:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:415:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:432:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:443:9: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 6; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:404:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 404 | _copy(inValue[0], *in.in1); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 4; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:422:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 422 | _copy(inValue[5], *in.in3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe, seqan::Merger7Multi >::_copy(TSkewDCStream&, const seqan::Triple >, seqan::Tag >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T = seqan::SimpleType; unsigned int SIZE = 5; TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >; TSkewDCStream = seqan::SkewDCStream >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:431:11: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | _copy(inValue[6], *in.in4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: required from ‘seqan::Pipe, seqan::Merger7Multi >& seqan::Pipe, seqan::Merger7Multi >::operator++() [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 464 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 431 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:801:108: required from ‘void seqan::assign(String&, Pipe&) [with TValue = Pair >; TStringSpec = Alloc<>; TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 801 | for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:826:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:385:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 385 | memcpy(&dst.i.i1, &src.i1, sizeof(T1)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: ‘struct seqan::Pair >’ declared here 95 | struct Pair | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1641:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1641 | _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1213:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = SimpleType*; TSource2 = SimpleType*]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1213 | arrayMoveBackward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1660:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const True&) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1660 | arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1681:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = SimpleType; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1681 | _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:856:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1048:30: required from ‘typename seqan::Size >::Type seqan::resizeSpace(String&, TSize, TBeginPosition, TEndPosition, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize = int; TBeginPosition = int; TEndPosition = unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1048 | TSize_ ret_ = _clearSpace( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^ 1049 | me, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~ 1050 | static_cast(size), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 1051 | static_cast(pos_begin), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1052 | static_cast(pos_end), /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1053 | tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2212:23: required from ‘TSize seqan::resizeSpace(T&, TSize, TBeginPosition, TEndPosition) [with T = String >; TSize = int; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 2212 | return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2267:16: required from ‘void seqan::erase(T&, TBeginPosition, TEndPosition) [with T = String >; TBeginPosition = int; TEndPosition = unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 2267 | resizeSpace(me, 0, pos, pos_end); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/general_processing.h:716:22: required from ‘void preTrim(TSeqs&, TIds&, TMulti&, unsigned int, unsigned int, unsigned int, GeneralStats&) [with TSeqs = seqan::StringSet > >; TIds = seqan::StringSet > >; TMulti = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 716 | erase(seqs[i], 0, head); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1607:24: required from ‘void preprocessingStage(TSeqs&, TIds&, DemultiplexingParams&, ProcessingParams&, const seqan::ArgumentParser&, GeneralStats&) [with TSeqs = seqan::StringSet > >; TIds = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 1607 | preTrim(seqs, ids, demultiplexingParams.multiplex, processingParams.trimLeft, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1608 | processingParams.trimRight, processingParams.minLen, generalStats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2655:35: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: 2655 | preprocessingStage(seqSet[0], idSet[0], demultiplexingParams, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2656 | processingParams, parser, generalStats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:95:8: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1621:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1621 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h: In instantiation of ‘void seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> > >, IndexEsa<> >; TSource = Index, Alloc<> > >, IndexEsa<> >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:730:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> > >, IndexEsa<> >; TValue2 = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 730 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:674:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> > >, IndexEsa<> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 674 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/holder_tristate.h:990:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> > >, IndexEsa<> >; typename Reference > >::Type = Index, Alloc<> > >, IndexEsa<> >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 990 | create(me); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:118:15: required from ‘typename seqan::Parameter_ >::Type seqan::container(Finder, TSpecFinder>&) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; typename Parameter_ >::Type = Index, Alloc<> > >, IndexEsa<> >&]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 118 | return value(me.index); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/find/find_base.h:1165:18: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/find_index.h:292:19: required from ‘bool seqan::find(Finder, TSpecFinder>&, const TPattern&) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecFinder = const Tag; TPattern = String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 292 | _findFirstIndex(finder, needle(pattern), TSpecFinder()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:274:10: required from ‘int findExactIndex(const TPrefix&, TFinder&) [with TPrefix = seqan::String >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 274 | if (find(finder, prefix)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:326:33: required from ‘void findAllExactIndex(seqan::String&, const TPrefices&, const TFinder&, TStats&) [with TPrefices = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TStats = DemultiplexStats]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 326 | int hit = findExactIndex(prefices[i], finderSet[tid]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/demultiplex.h:458:19: required from ‘void doAll(seqan::StringSet >&, TMultiplex&, TBarcodes&, TFinder&, DemultiplexStats&, bool) [with TBarcodes = seqan::StringSet, seqan::Alloc<> > >; TMultiplex = seqan::StringSet > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 458 | findAllExactIndex(matches, multiplex, esaFinder, stats); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:1733:14: required from ‘int demultiplexingStage(DemultiplexingParams&, TSeqsVec&, TIdsVec&, TFinder&, TMap&, GeneralStats&) [with TSeqsVec = seqan::String > > >; TIdsVec = seqan::String > > >; TFinder = seqan::Finder, seqan::Alloc<> > >, seqan::IndexEsa<> > >; TMap = seqan::String]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 1733 | doAll(groups, params.multiplex, params.barcodes, esaFinder, params.stats, params.exclude); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2659:40: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: 2659 | if (demultiplexingStage(demultiplexingParams, seqSet, idSet, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2660 | esaFinder, map, generalStats) != 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/fundamental_transport.h:133:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >& seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >::operator=(const seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >&)’ is deprecated [-Wdeprecated-copy] 133 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: because ‘seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]’ 548 | Index(Index const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value > >::Type& seqan::Pipe >::operator*() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>; typename seqan::Value > >::Type = seqan::Pair >, long unsigned int, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:148:22: required from ‘const typename seqan::Value > >::Type seqan::Pipe >::operator*() const [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >; typename seqan::Value > >::Type = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 148 | return F(*in); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:24: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_esa_base.h:548:17: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:134:20: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 134 | tmp.i1 = getValueI1(*in); | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NCompMulti >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Namer >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti >, long unsigned int, seqan::Tag >, seqan::String >, long unsigned int, seqan::Pair > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 328 | names_sliced << slicedPos; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_separator7.h:64:9: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TFunctor = _skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > >; TOut1 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut2 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut4 = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 64 | push(out4, i); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:342:25: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 342 | _skew7SeparateSlices( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~^ 343 | names_sliced, func_slice, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 344 | names_S1, names_S2, names_S4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:416:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:294:11: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:651:23: required from ‘bool seqan::control(Pipe&, const TCommand&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >; TCommand = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 651 | return control(me.in, command); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >; TSpec = Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tuple, 7, BitPacked<> >, Tag >, SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NCompMulti >, Tuple, 7, BitPacked<> >, Tag >, int> > >, Filter<_skew7GlobalSlicedMulti >, long unsigned int, Tag >, String >, long unsigned int, Pair > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >& seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tuple, 7, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple, 7, seqan::BitPacked<> >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:165:23: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 165 | me.tmp.i1 = me.last.i1; | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:401:106: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 341 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 352 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7_multi.h:367:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(PairDecrementer_&, const TLimits2&) [with TPair = Pair >; TLimits = String >; unsigned int m = 7; TLimits2 = String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:537:11: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 537 | setHost(localPos, limits); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:1119:16: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 1119 | me.pos = TPair(0, 0); | ~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:544:13: required from ‘void seqan::Pipe >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 544 | fill(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:613:19: required from ‘bool seqan::control(Pipe, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; unsigned int m = 7; TPack = BitPacked<>; TPair = Pair >; TLimitsString = String >; ControlBeginRead = Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 613 | me.prepare(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TSpec = Multi >, Pair >, String > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tuple, 7, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, 7, BitPacked<> >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >, Multi >, Pair >, String > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_sampler.h:557:32: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 557 | tmp.i1 = localPos; | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew7NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew7NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h: In instantiation of ‘TResult seqan::_skew7NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew7NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 345 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:312:11: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<7, Tag > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:335:20: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 148 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:362:29: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 247 | TNames_Sliced names_sliced(map_sliced); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:143:22: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 143 | last = *in; | ~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:684:24: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 684 | else handler2->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:953:16: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 953 | writer->end(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:837:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 837 | endWrite(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 259 | TNames_Linear_Unique names_linear(map_linear); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:584:58: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 584 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:376:34: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_aggregate.h:59: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:124:27: required from ‘bool seqan::CompareSkewDCStream::operator()(const seqan::SkewDCStream&, const seqan::SkewDCStream&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 124 | if (a.i.i3[i] < b.i.i3[i]) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:307:23: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 307 | if (!streamGreater(inValue[stream],inValue[rank[right]])) break; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: required from ‘seqan::Pipe, seqan::Merger7>& seqan::Pipe, seqan::Merger7>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 319 | insertStream(rank[first]); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:440:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 440 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_counter.h:105:13: required from ‘seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >, seqan::Skew7>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 105 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:620:9: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:446:6: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 446 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:464:4: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew7NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(Pipe >&, const ControlBeginRead&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TCompare = _skew3NComp >, Tag >, int>; ControlBeginRead = Tag]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:712:23: required from ‘bool seqan::beginRead(Pipe&) [with TInput = Pool >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >; TSpec = Namer<_skew3NComp >, Tag >, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 712 | return control(me, ControlBeginRead()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1354:23: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1354 | if (!beginRead(src)) return false; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:164:21: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 164 | me.last = *me.in; | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h: In instantiation of ‘TResult seqan::_skew3NComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Pair >, seqan::Tag >; TResult = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_namer.h:141:30: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TCompare = seqan::_skew3NComp >, seqan::Tag >, int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 141 | if (!eof(in) && C(last, *in) != 0) { /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 251 | names_sliced << namer; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:74:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 74 | const TStoredValue *sa = a.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: taking address of packed member of ‘seqan::Tuple >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 75 | const TStoredValue *sb = b.i2.i; | ~~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:75:43: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:218:11: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew7NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_filter.h:153:13: required from ‘seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TFunctor = seqan::filterI2 >, long unsigned int>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 153 | ++in; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_sa_lss.h:415:29: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tag >, seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Pair >, seqan::Tag >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: required from ‘bool seqan::operator<<(Pool&, TSource&) [with TValue = Pair >, Tag >; TSpec = SorterSpec >, Tag >, int>, long unsigned int, File > > >; TSource = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >, Sampler<3> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1395 | return assign(dest, src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:241:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:937:18: warning: implicitly-declared ‘constexpr seqan::Pair >, seqan::Tag >& seqan::Pair >, seqan::Tag >::operator=(const seqan::Pair >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 937 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >, seqan::Tag >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = seqan::Tuple >]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapLinear >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 86 | o2.i2[0] = (*nameIn).i2; ++nameIn; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:269:29: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pipe >, Tag >, SorterSpec >, Tag >, int>, long unsigned int, File > > > >, Namer<_skew3NComp >, Tag >, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Pair >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:673:41: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 673 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:361:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 361 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair >; TConfig = seqan::MapperConfigSize >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:674:25: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Pair >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 674 | else handler2->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:930:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 930 | writer->push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1191:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1191 | me.push(Val_); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1356:17: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1356 | push(dest, *src); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: required from ‘bool seqan::assign(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 1388 | return beginWrite(dest) && append(dest, src) && endWrite(dest); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1395:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:567:33: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 567 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:301:6: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 301 | ++in.in5; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger7.h:319:4: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Pair >; TConfig = MapperConfigSize<_skew3NMapSliced >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1357:13: required from ‘bool seqan::append(Pool&, TSource&) [with TValue = Pair >; TSpec = MapperSpec >, long unsigned int>, long unsigned int, File > > >; TSource = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1357 | ++src; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:1388:42: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Pair >& seqan::Pair >::operator=(const seqan::Pair >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: because ‘seqan::Pair >’ has user-provided ‘seqan::Pair >::Pair(const seqan::Pair >&) [with T1 = long unsigned int; T2 = long unsigned int]’ 110 | SEQAN_HOST_DEVICE Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {} | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:387:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 387 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:607:32: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 607 | else return handler2->next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pipe_base.h:919:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | buffer = handler.next(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_base.h:919:15: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 919 | reader->pop(); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew3.h:329:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/pair_packed.h:110:23: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:252:50: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 252 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:253:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 253 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_mapper.h:293:46: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 293 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 103 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 6; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 3; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:68:21: required from ‘bool seqan::AdaptorCompare2Less::operator()(const typename TCompare::first_argument_type&, const typename TCompare::second_argument_type&) const [with TCompare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 3, int>; typename TCompare::first_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >; typename TCompare::second_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 68 | return C(a, b) < 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~^~~~~~ /usr/include/c++/14/bits/predefined_ops.h:158:30: required from ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Iterator2 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = seqan::AdaptorCompare2Less, seqan::Tuple >, seqan::Tag >, 3, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 158 | { return bool(_M_comp(*__it1, *__it2)); } /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1771:14: required from ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 3, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1771 | if (__comp(__i, __first)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1811:25: required from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 3, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 1811 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1902:31: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/triple_packed.h:103:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 4; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 1; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:68:21: required from ‘bool seqan::AdaptorCompare2Less::operator()(const typename TCompare::first_argument_type&, const typename TCompare::second_argument_type&) const [with TCompare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 1, int>; typename TCompare::first_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >; typename TCompare::second_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 68 | return C(a, b) < 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~ /usr/include/c++/14/bits/predefined_ops.h:158:30: required from ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Iterator2 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = seqan::AdaptorCompare2Less, seqan::Tuple >, seqan::Tag >, 1, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 158 | { return bool(_M_comp(*__it1, *__it2)); } /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1771:14: required from ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 1, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1771 | if (__comp(__i, __first)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1811:25: required from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 1, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1811 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1902:31: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h: In instantiation of ‘const typename seqan::StoredTupleValue_::Type& seqan::Tuple >::operator[](TPos) const [with TPos = unsigned int; TValue = long unsigned int; unsigned int SIZE = 5; typename seqan::StoredTupleValue_::Type = long unsigned int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_skew7.h:191:25: required from ‘TResult seqan::_skew7ExtendComp::operator()(const TValue&, const TValue&) const [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; unsigned int EXT_LENGTH = 2; TResult = int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 191 | if (a.i3[i] == b.i3[i]) continue; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/pipe/pool_sorter.h:68:21: required from ‘bool seqan::AdaptorCompare2Less::operator()(const typename TCompare::first_argument_type&, const typename TCompare::second_argument_type&) const [with TCompare = seqan::_skew7ExtendComp, seqan::Tuple >, seqan::Tag >, 2, int>; typename TCompare::first_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >; typename TCompare::second_argument_type = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 68 | return C(a, b) < 0; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~^~~~~~ /usr/include/c++/14/bits/predefined_ops.h:158:30: required from ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Iterator2 = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = seqan::AdaptorCompare2Less, seqan::Tuple >, seqan::Tag >, 2, int> >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 158 | { return bool(_M_comp(*__it1, *__it2)); } /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1771:14: required from ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 2, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1771 | if (__comp(__i, __first)) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1811:25: required from ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = seqan::Triple, seqan::Tuple >, seqan::Tag >*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, seqan::Tuple >, seqan::Tag >, 2, int> > >]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 1811 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1902:31: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:194:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc<> >; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 194 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:221:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = String >, Alloc<> >; TText = StringSet, Alloc<> > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 221 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:685:20: required from ‘bool seqan::indexCreate(Index&, FibreSA, TSpecAlg) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TSpecAlg = Skew7; FibreSA = const Tag]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 685 | createSuffixArray(indexSA(index), indexText(index), alg); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexCreate(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 726 | return indexCreate(index, fibre, typename DefaultIndexCreator, Tag const>::Type()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/index_shims.h:835:21: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> > >; TSpec = IndexEsa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 835 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexlib.cpp:2358:25: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: 2358 | indexRequire(indexSet, FibreSA()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/tuple_base.h:171:17: warning: returning reference to temporary [-Wreturn-local-addr] 171 | return i[k]; | ~^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io.h:64: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h: In member function ‘void seqan::SequenceStreamImpl_::_guessFileTypeAndFormatForReadingAndInitialize()’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:310:25: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | _fileFormat = this->_checkFormat(*_istreamReader); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/seq_io/sequence_stream_impl.h:313:9: note: here 313 | case SeqIOFileType_::FILE_TYPE_AUTO: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:142:117: warning: this statement may fall through [-Wimplicit-fallthrough=] 142 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:144:9: note: here 144 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:145:118: warning: this statement may fall through [-Wimplicit-fallthrough=] 145 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:147:9: note: here 147 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:149:103: warning: this statement may fall through [-Wimplicit-fallthrough=] 149 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:151:9: note: here 151 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:152:119: warning: this statement may fall through [-Wimplicit-fallthrough=] 152 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p--; | ~~~~~~^~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:154:9: note: here 154 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:156:105: warning: this statement may fall through [-Wimplicit-fallthrough=] 156 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:158:9: note: here 158 | case 1: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h: In function ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> > > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:395:130: warning: this statement may fall through [-Wimplicit-fallthrough=] 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:397:25: note: here 397 | case 5: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:398:131: warning: this statement may fall through [-Wimplicit-fallthrough=] 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:400:25: note: here 400 | case 4: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:402:162: warning: this statement may fall through [-Wimplicit-fallthrough=] 402 | cp___(o4,0,cp___(o5,1,cp___(o6,2, *textIn))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:404:25: note: here 404 | case 3: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:405:132: warning: this statement may fall through [-Wimplicit-fallthrough=] 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p; | ^~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:407:25: note: here 407 | case 2: | ^~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:409:138: warning: this statement may fall through [-Wimplicit-fallthrough=] 409 | cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4, *textIn))))); ++textIn; | ^~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/index/pump_extender7.h:411:25: note: here 411 | case 1: | ^~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io.h:59, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/store.h:41: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h: In function ‘void seqan::_assignTagsBamToSamOneTag(TTarget&, TSourceIter&) [with TTarget = String >; TSourceIter = Iter >, AdaptorIterator > >]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 399 | snprintf(buffer, 4, "%d", x); | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/bam_io/bam_sam_conversion.h:399:21: note: ‘snprintf’ output between 2 and 5 bytes into a destination of size 4 399 | snprintf(buffer, 4, "%d", x); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 88%] Linking CXX static library libseqan_flexlib.a cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -P CMakeFiles/seqan_flexlib.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_flexlib.dir/link.txt --verbose=1 /usr/bin/ar qc libseqan_flexlib.a CMakeFiles/seqan_flexlib.dir/seqan_flexlib.cpp.o /usr/bin/ranlib libseqan_flexlib.a make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 88%] Built target seqan_flexlib make -f extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 88%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/seqan_flexbar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DFLEX_PROG=QUALITY_CONTROL -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/seqan_flexbar.cpp.o -MF CMakeFiles/sflexQC.dir/seqan_flexbar.cpp.o.d -o CMakeFiles/sflexQC.dir/seqan_flexbar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexbar.cpp [ 90%] Linking CXX executable ../../../bin/sflexQC cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/sflexQC.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sflexQC.dir/seqan_flexbar.cpp.o -o ../../../bin/sflexQC libseqan_flexlib.a -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 90%] Built target sflexQC make -f extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 91%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/seqan_flexbar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DFLEX_PROG=ADAPTER_REMOVAL -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/seqan_flexbar.cpp.o -MF CMakeFiles/sflexAR.dir/seqan_flexbar.cpp.o.d -o CMakeFiles/sflexAR.dir/seqan_flexbar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexbar.cpp [ 91%] Linking CXX executable ../../../bin/sflexAR cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/sflexAR.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sflexAR.dir/seqan_flexbar.cpp.o -o ../../../bin/sflexAR libseqan_flexlib.a -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 91%] Built target sflexAR make -f extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 93%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/seqan_flexbar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DFLEX_PROG=DEMULTIPLEXING -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/seqan_flexbar.cpp.o -MF CMakeFiles/sflexDMulti.dir/seqan_flexbar.cpp.o.d -o CMakeFiles/sflexDMulti.dir/seqan_flexbar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexbar.cpp [ 93%] Linking CXX executable ../../../bin/sflexDMulti cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/sflexDMulti.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sflexDMulti.dir/seqan_flexbar.cpp.o -o ../../../bin/sflexDMulti libseqan_flexlib.a -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 93%] Built target sflexDMulti make -f extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 95%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/seqan_flexbar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DFLEX_PROG=FILTERING -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/seqan_flexbar.cpp.o -MF CMakeFiles/sflexFilter.dir/seqan_flexbar.cpp.o.d -o CMakeFiles/sflexFilter.dir/seqan_flexbar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexbar.cpp [ 95%] Linking CXX executable ../../../bin/sflexFilter cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/sflexFilter.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sflexFilter.dir/seqan_flexbar.cpp.o -o ../../../bin/sflexFilter libseqan_flexlib.a -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 95%] Built target sflexFilter make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 95%] Building CXX object extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/seqan_flexbar.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/g++ -DSEQAN_DATE=\"\" -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/seqan_flexbar.cpp.o -MF CMakeFiles/seqan_flexbar.dir/seqan_flexbar.cpp.o.d -o CMakeFiles/seqan_flexbar.dir/seqan_flexbar.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar/seqan_flexbar.cpp [ 96%] Linking CXX executable ../../../bin/seqan_flexbar cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_flexbar.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/seqan_flexbar.dir/seqan_flexbar.cpp.o -o ../../../bin/seqan_flexbar libseqan_flexlib.a -lrt -L/usr/lib64 -lz -L/usr/lib64 -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 96%] Built target seqan_flexbar make -f extras/apps/sgip/CMakeFiles/sgip.dir/build.make extras/apps/sgip/CMakeFiles/sgip.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/sgip /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/sgip/CMakeFiles/sgip.dir/build.make extras/apps/sgip/CMakeFiles/sgip.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 96%] Building CXX object extras/apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/sgip && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o -MF CMakeFiles/sgip.dir/sgip.cpp.o.d -o CMakeFiles/sgip.dir/sgip.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip/sgip.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream.h:86, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_types.h:43, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip/sgip.cpp:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/debug_test_system.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip/sgip.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip/sgip_base.h:33, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip/sgip.cpp:33: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [ 98%] Linking CXX executable ../../../bin/sgip cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/sgip && /usr/bin/cmake -E cmake_link_script CMakeFiles/sgip.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -std=c++11 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/sgip.dir/sgip.cpp.o -o ../../../bin/sgip -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 98%] Built target sgip make -f extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build.make extras/apps/variant_comp/CMakeFiles/variant_comp.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/variant_comp /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/variant_comp/CMakeFiles/variant_comp.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make -f extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build.make extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 98%] Building CXX object extras/apps/variant_comp/CMakeFiles/variant_comp.dir/variant_comp.cpp.o cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/variant_comp && /usr/bin/g++ -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_EXECINFO=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-1.4.2/extras/include -I/builddir/build/BUILD/seqan-1.4.2/core/include -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -MD -MT extras/apps/variant_comp/CMakeFiles/variant_comp.dir/variant_comp.cpp.o -MF CMakeFiles/variant_comp.dir/variant_comp.cpp.o.d -o CMakeFiles/variant_comp.dir/variant_comp.cpp.o -c /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier.h:68, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:48, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:80:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 80 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:151:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 151 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:220:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 220 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:229:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:239:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 239 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:249:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 249 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:259:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:268:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/modifier/modifier_functors.h:280:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 280 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/stream_algorithms.h:40, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:91: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamPeek(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:169:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 169 | if (c == EOF) | ^ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h: In function ‘int seqan::streamReadChar(char&, FILE*)’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/stream/adapt_cstdio.h:182:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 182 | if (c == EOF) | ^ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file.h:117: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h: At global scope: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/file/string_external.h:1436:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1436 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:46, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:47, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:33: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:342:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms.h:47: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_algorithms/graph_algorithm.h:793:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 793 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:35: /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:238:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 238 | struct LessGPosSize : public ::std::binary_function < TIndel, TIndel, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:256:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | struct LessGPos : public ::std::binary_function < TVariant, TVariant, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h: In function ‘bool seqan::compareIndelPair(TIndel&, TIndel&, TOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:278:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 278 | if(options.genotypeAware && predIndel.genotype != refIndel.genotype) | ^~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:281:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 281 | int sizeTol = int((double)abs(refIndel.indelSize) * options.sizeTolerance); | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h: In function ‘int seqan::compareIndels(TIndelSet&, TIndelSet&, TGenome&, TGenomeIDs&, TOptions&)’: /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:477:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 477 | for(TIndelIt it = begin(refIndels); it != end(refIndels); ++it) | ^~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 479 | for(TIndelIt it = begin(predIndels); it != end(predIndels); ++it) | ^~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/graph_align.h:55: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h: In instantiation of ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = int]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1917:15: required from ‘void seqan::findIntervals(const Graph&, const TPropertyMap&, TValue, TValue, String&) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = int; TCargo = int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: 1917 | findIntervals(g, pm, act_knot, query_begin, query_end, result); /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1898:15: required from ‘void seqan::findIntervals(const IntervalTree&, TValue, TValue, String&) [with TValue = int; TCargo = int]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: 1898 | findIntervals(tree.g,tree.pm,query_begin,query_end,result); /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:582:17: required from ‘int seqan::compareIndels(TIndelSet&, TIndelSet&, TGenome&, TGenomeIDs&, TOptions&) [with TIndelSet = StringSet; TGenome = StringSet, Alloc<> > >; TGenomeIDs = String > >; TOptions = IndelCompareOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: 582 | findIntervals(itree,beginPoint,endPoint,intersectingIntervals); /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:834:31: required from here /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: 834 | int result = compareIndels(refIndels,predictedIndels,genomes,genomeIDs,options); /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.h:479:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1949:26: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1949 | act_prop = property(pm,act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1961:43: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1961 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:1982:51: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1982 | next_prop = property(pm,targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 398 | IntervalTreeNode(IntervalTreeNode const & other): | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_fundamental.h:79, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence.h:51, from /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:29: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]’: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1542 | _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1398 | arrayCopyForward(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = SimpleType; TValueTarget = SimpleType]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1429 | _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1840 | arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = SimpleType; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 1855 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 131 | reserve(*this, std::min(capacity(source), computeGenerousCapacity(source, length(source))), Exact()); /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:444:39: required from ‘int readGFF(const char*, TIndelSet&, TSnpSet&, TGenomeMap&, TOptions&) [with TIndelSet = seqan::StringSet; TSnpSet = seqan::StringSet; TGenomeMap = std::map >, unsigned int>; TOptions = seqan::IndelCompareOptions<>]’ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 444 | TIndel indel = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}; /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ^ /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp/variant_comp.cpp:815:16: required from here /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: 815 | if (readGFF(toCString(options.inputReference), refIndels, refSnps, gIdStringToIdNumMap, options) > 0) /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/misc/misc_interval_tree.h:398:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_alphabet.h:84, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:68: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/basic_allocator.h:53, from /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic.h:74: In function ‘void seqan::allocate(T&, TValue*&, TSize, const Tag&) [with T = String, Alloc<> >; TValue = std::__cxx11::basic_string; TSize = long unsigned int; TUsage = AllocateStorage_]’, inlined from ‘typename seqan::Value > >::Type* seqan::_allocateStorage(String >&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = void; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_alloc.h:385:13, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1685:28, inlined from ‘typename seqan::Value >::Type* seqan::_reallocateStorage(String&, TSize, Generous) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1730:30, inlined from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1835:83, inlined from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1855:20, inlined from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc<> >; TExpand = seqan::Tag]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1887:45, inlined from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = std::__cxx11::basic_string; TSpec = Alloc<>; TSize = long unsigned int; TExpand = TagGenerous_]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/string_base.h:1952:50, inlined from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc<> >; TSize = long unsigned int]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2143:18, inlined from ‘void seqan::eraseBack(T&) [with T = String, Alloc<> >]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/sequence/sequence_interface.h:2337:8, inlined from ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’ at /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-1.4.2/core/include/seqan/basic/allocator_interface.h:297:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 297 | */ data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/exception_ptr.h:38, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41: /usr/include/c++/14/new: In function ‘TSequence seqan::_toText(const TSequence&) [with TSequence = std::__cxx11::basic_string]’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ [100%] Linking CXX executable ../../../bin/variant_comp cd /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/variant_comp && /usr/bin/cmake -E cmake_link_script CMakeFiles/variant_comp.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -lemon -W -Wall -Wno-long-long -fstrict-aliasing -Wstrict-aliasing -pedantic -Wno-variadic-macros -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DSEQAN_ENABLE_DEBUG=0 -static-libgcc -static-libstdc++ -rdynamic CMakeFiles/variant_comp.dir/variant_comp.cpp.o -o ../../../bin/variant_comp -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [100%] Built target variant_comp make[1]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-1.4.2/build/Release/CMakeFiles 0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.72WaOI + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le '!=' / ']' + rm -rf /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le ++ dirname /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd seqan-1.4.2 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le 'INSTALL=/usr/bin/install -p' -C build/Release make: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-1.4.2 -B/builddir/build/BUILD/seqan-1.4.2/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-1.4.2/build/Release/CMakeFiles /builddir/build/BUILD/seqan-1.4.2/build/Release//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/CMakeFiles/seqan_core.dir/build.make core/CMakeFiles/seqan_core.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core /builddir/build/BUILD/seqan-1.4.2/build/Release/core/CMakeFiles/seqan_core.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/CMakeFiles/seqan_core.dir/build.make core/CMakeFiles/seqan_core.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/CMakeFiles/seqan_core.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 0%] Built target seqan_core /usr/bin/make -f core/apps/dfi/CMakeFiles/dfi.dir/build.make core/apps/dfi/CMakeFiles/dfi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/dfi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/dfi /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/dfi/CMakeFiles/dfi.dir/build.make core/apps/dfi/CMakeFiles/dfi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/dfi/CMakeFiles/dfi.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 1%] Built target dfi /usr/bin/make -f core/apps/fiona/CMakeFiles/compute_gain.dir/build.make core/apps/fiona/CMakeFiles/compute_gain.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona/CMakeFiles/compute_gain.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/fiona/CMakeFiles/compute_gain.dir/build.make core/apps/fiona/CMakeFiles/compute_gain.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/fiona/CMakeFiles/compute_gain.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 3%] Built target compute_gain /usr/bin/make -f core/apps/fiona/CMakeFiles/fiona.dir/build.make core/apps/fiona/CMakeFiles/fiona.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona/CMakeFiles/fiona.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/fiona/CMakeFiles/fiona.dir/build.make core/apps/fiona/CMakeFiles/fiona.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/fiona/CMakeFiles/fiona.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 4%] Built target fiona /usr/bin/make -f core/apps/fiona/CMakeFiles/fiona_illumina.dir/build.make core/apps/fiona/CMakeFiles/fiona_illumina.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/fiona/CMakeFiles/fiona_illumina.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/fiona/CMakeFiles/fiona_illumina.dir/build.make core/apps/fiona/CMakeFiles/fiona_illumina.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/fiona/CMakeFiles/fiona_illumina.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 6%] Built target fiona_illumina /usr/bin/make -f core/apps/mason/CMakeFiles/mason.dir/build.make core/apps/mason/CMakeFiles/mason.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/mason /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/mason /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/mason/CMakeFiles/mason.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/mason/CMakeFiles/mason.dir/build.make core/apps/mason/CMakeFiles/mason.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/mason/CMakeFiles/mason.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 8%] Built target mason /usr/bin/make -f core/apps/micro_razers/CMakeFiles/micro_razers.dir/build.make core/apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/micro_razers /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/micro_razers/CMakeFiles/micro_razers.dir/build.make core/apps/micro_razers/CMakeFiles/micro_razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/micro_razers/CMakeFiles/micro_razers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 9%] Built target micro_razers /usr/bin/make -f core/apps/pair_align/CMakeFiles/pair_align.dir/build.make core/apps/pair_align/CMakeFiles/pair_align.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/pair_align /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/pair_align /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/pair_align/CMakeFiles/pair_align.dir/build.make core/apps/pair_align/CMakeFiles/pair_align.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/pair_align/CMakeFiles/pair_align.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 11%] Built target pair_align /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 12%] Built target rabema_prepare_sam /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 14%] Built target rabema_build_gold_standard /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make core/apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/rabema/CMakeFiles/rabema_evaluate.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 16%] Built target rabema_evaluate /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_do_search.dir/build.make core/apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/rabema/CMakeFiles/rabema_do_search.dir/build.make core/apps/rabema/CMakeFiles/rabema_do_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/rabema/CMakeFiles/rabema_do_search.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 16%] Built target rabema_do_search /usr/bin/make -f core/apps/razers/CMakeFiles/razers.dir/build.make core/apps/razers/CMakeFiles/razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/razers /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/razers/CMakeFiles/razers.dir/build.make core/apps/razers/CMakeFiles/razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/razers/CMakeFiles/razers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 19%] Built target razers /usr/bin/make -f core/apps/razers2/CMakeFiles/razers2.dir/build.make core/apps/razers2/CMakeFiles/razers2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/razers2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2 /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/razers2/CMakeFiles/razers2.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/razers2/CMakeFiles/razers2.dir/build.make core/apps/razers2/CMakeFiles/razers2.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/razers2/CMakeFiles/razers2.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 20%] Built target razers2 /usr/bin/make -f core/apps/sak/CMakeFiles/sak.dir/build.make core/apps/sak/CMakeFiles/sak.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/sak/CMakeFiles/sak.dir/build.make core/apps/sak/CMakeFiles/sak.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/sak/CMakeFiles/sak.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 22%] Built target sak /usr/bin/make -f core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/sam2matrix /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sam2matrix /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/sam2matrix/CMakeFiles/sam2matrix.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 24%] Built target sam2matrix /usr/bin/make -f core/apps/samcat/CMakeFiles/samcat.dir/build.make core/apps/samcat/CMakeFiles/samcat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/samcat /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/samcat /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/samcat/CMakeFiles/samcat.dir/build.make core/apps/samcat/CMakeFiles/samcat.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/samcat/CMakeFiles/samcat.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 25%] Built target samcat /usr/bin/make -f core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/seqan_tcoffee /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqan_tcoffee /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 25%] Built target seqan_tcoffee /usr/bin/make -f core/apps/seqcons/CMakeFiles/seqcons.dir/build.make core/apps/seqcons/CMakeFiles/seqcons.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/seqcons /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqcons /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/seqcons/CMakeFiles/seqcons.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/seqcons/CMakeFiles/seqcons.dir/build.make core/apps/seqcons/CMakeFiles/seqcons.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/seqcons/CMakeFiles/seqcons.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 27%] Built target seqcons /usr/bin/make -f core/apps/snp_store/CMakeFiles/snp_store.dir/build.make core/apps/snp_store/CMakeFiles/snp_store.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/snp_store /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/snp_store /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/snp_store/CMakeFiles/snp_store.dir/build.make core/apps/snp_store/CMakeFiles/snp_store.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/snp_store/CMakeFiles/snp_store.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 29%] Built target snp_store /usr/bin/make -f core/apps/splazers/CMakeFiles/splazers.dir/build.make core/apps/splazers/CMakeFiles/splazers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/splazers /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/splazers /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/splazers/CMakeFiles/splazers.dir/build.make core/apps/splazers/CMakeFiles/splazers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/splazers/CMakeFiles/splazers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 29%] Built target splazers /usr/bin/make -f core/apps/stellar/CMakeFiles/stellar.dir/build.make core/apps/stellar/CMakeFiles/stellar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/stellar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/stellar /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/stellar/CMakeFiles/stellar.dir/build.make core/apps/stellar/CMakeFiles/stellar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/stellar/CMakeFiles/stellar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 30%] Built target stellar /usr/bin/make -f core/apps/tree_recon/CMakeFiles/tree_recon.dir/build.make core/apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/tree_recon /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/tree_recon /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f core/apps/tree_recon/CMakeFiles/tree_recon.dir/build.make core/apps/tree_recon/CMakeFiles/tree_recon.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'core/apps/tree_recon/CMakeFiles/tree_recon.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target tree_recon /usr/bin/make -f extras/CMakeFiles/seqan_extras.dir/build.make extras/CMakeFiles/seqan_extras.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/CMakeFiles/seqan_extras.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/CMakeFiles/seqan_extras.dir/build.make extras/CMakeFiles/seqan_extras.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/CMakeFiles/seqan_extras.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target seqan_extras /usr/bin/make -f extras/apps/alf/CMakeFiles/alf.dir/build.make extras/apps/alf/CMakeFiles/alf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/alf /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/alf /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/alf/CMakeFiles/alf.dir/build.make extras/apps/alf/CMakeFiles/alf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/alf/CMakeFiles/alf.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target alf /usr/bin/make -f extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build.make extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/breakpoint_calculator /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/breakpoint_calculator /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build.make extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/breakpoint_calculator/CMakeFiles/breakpoint_calculator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 32%] Built target breakpoint_calculator /usr/bin/make -f extras/apps/bs_tools/CMakeFiles/bisar.dir/build.make extras/apps/bs_tools/CMakeFiles/bisar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/bs_tools/CMakeFiles/bisar.dir/build.make extras/apps/bs_tools/CMakeFiles/bisar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/bs_tools/CMakeFiles/bisar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 33%] Built target bisar /usr/bin/make -f extras/apps/bs_tools/CMakeFiles/casbar.dir/build.make extras/apps/bs_tools/CMakeFiles/casbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/bs_tools/CMakeFiles/casbar.dir/build.make extras/apps/bs_tools/CMakeFiles/casbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/bs_tools/CMakeFiles/casbar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 35%] Built target casbar /usr/bin/make -f extras/apps/bs_tools/CMakeFiles/four2three.dir/build.make extras/apps/bs_tools/CMakeFiles/four2three.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/bs_tools/CMakeFiles/four2three.dir/build.make extras/apps/bs_tools/CMakeFiles/four2three.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/bs_tools/CMakeFiles/four2three.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 37%] Built target four2three /usr/bin/make -f extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 38%] Built target fx_bam_coverage /usr/bin/make -f extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 38%] Built target fx_fastq_stats /usr/bin/make -f extras/apps/gustaf/CMakeFiles/gustaf.dir/build.make extras/apps/gustaf/CMakeFiles/gustaf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/gustaf /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/gustaf /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/gustaf/CMakeFiles/gustaf.dir/build.make extras/apps/gustaf/CMakeFiles/gustaf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/gustaf/CMakeFiles/gustaf.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 40%] Built target gustaf /usr/bin/make -f extras/apps/insegt/CMakeFiles/insegt.dir/build.make extras/apps/insegt/CMakeFiles/insegt.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/insegt /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/insegt /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/insegt/CMakeFiles/insegt.dir/build.make extras/apps/insegt/CMakeFiles/insegt.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/insegt/CMakeFiles/insegt.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 41%] Built target insegt /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_sim.dir/build.make extras/apps/mason2/CMakeFiles/mason_sim.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_sim.dir/build.make extras/apps/mason2/CMakeFiles/mason_sim.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_sim.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 50%] Built target mason_sim /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_genome.dir/build.make extras/apps/mason2/CMakeFiles/mason_genome.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_genome.dir/build.make extras/apps/mason2/CMakeFiles/mason_genome.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_genome.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 51%] Built target mason_genome /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_methylation.dir/build.make extras/apps/mason2/CMakeFiles/mason_methylation.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_methylation.dir/build.make extras/apps/mason2/CMakeFiles/mason_methylation.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_methylation.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 51%] Built target mason_methylation /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 53%] Built target mason_frag_sequencing /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_variator.dir/build.make extras/apps/mason2/CMakeFiles/mason_variator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_variator.dir/build.make extras/apps/mason2/CMakeFiles/mason_variator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_variator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 54%] Built target mason_variator /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_materializer.dir/build.make extras/apps/mason2/CMakeFiles/mason_materializer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_materializer.dir/build.make extras/apps/mason2/CMakeFiles/mason_materializer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_materializer.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 56%] Built target mason_materializer /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_simulator.dir/build.make extras/apps/mason2/CMakeFiles/mason_simulator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_simulator.dir/build.make extras/apps/mason2/CMakeFiles/mason_simulator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_simulator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 58%] Built target mason_simulator /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_splicing.dir/build.make extras/apps/mason2/CMakeFiles/mason_splicing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_splicing.dir/build.make extras/apps/mason2/CMakeFiles/mason_splicing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_splicing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 59%] Built target mason_splicing /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_tests.dir/build.make extras/apps/mason2/CMakeFiles/mason_tests.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/mason2/CMakeFiles/mason_tests.dir/build.make extras/apps/mason2/CMakeFiles/mason_tests.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/mason2/CMakeFiles/mason_tests.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 61%] Built target mason_tests /usr/bin/make -f extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 61%] Built target roi_plot_thumbnails /usr/bin/make -f extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/ngs_roi/CMakeFiles/bam2roi.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 64%] Built target bam2roi /usr/bin/make -f extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 67%] Built target roi_feature_projection /usr/bin/make -f extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/param_chooser/CMakeFiles/param_chooser.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 69%] Built target param_chooser /usr/bin/make -f extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 70%] Built target test_funcs_param_chooser /usr/bin/make -f extras/apps/razers3/CMakeFiles/razers3.dir/build.make extras/apps/razers3/CMakeFiles/razers3.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/razers3/CMakeFiles/razers3.dir/build.make extras/apps/razers3/CMakeFiles/razers3.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/razers3/CMakeFiles/razers3.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 72%] Built target razers3 /usr/bin/make -f extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 74%] Built target razers3_simulate_reads /usr/bin/make -f extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3 /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/razers3/CMakeFiles/razers3_quality2prob.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 75%] Built target razers3_quality2prob /usr/bin/make -f extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build.make extras/apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/rep_sep /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/rep_sep /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build.make extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/rep_sep/CMakeFiles/rep_sep.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 77%] Built target rep_sep /usr/bin/make -f extras/apps/searchjoin/CMakeFiles/search.dir/build.make extras/apps/searchjoin/CMakeFiles/search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin/CMakeFiles/search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/searchjoin/CMakeFiles/search.dir/build.make extras/apps/searchjoin/CMakeFiles/search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/searchjoin/CMakeFiles/search.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 79%] Built target search /usr/bin/make -f extras/apps/searchjoin/CMakeFiles/join.dir/build.make extras/apps/searchjoin/CMakeFiles/join.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/searchjoin/CMakeFiles/join.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/searchjoin/CMakeFiles/join.dir/build.make extras/apps/searchjoin/CMakeFiles/join.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/searchjoin/CMakeFiles/join.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 80%] Built target join /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/test_sflex_demultiplex.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 82%] Built target test_sflex_demultiplex /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/test_sflex_trimming.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 83%] Built target test_sflex_trimming /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/test_sflex_adapter.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 85%] Built target test_sflex_adapter /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/test_sflex_general_processing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 87%] Built target test_sflex_general_processing /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/seqan_flexlib.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 88%] Built target seqan_flexlib /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/sflexQC.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 90%] Built target sflexQC /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/sflexAR.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 91%] Built target sflexAR /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/sflexDMulti.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 93%] Built target sflexDMulti /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/sflexFilter.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 95%] Built target sflexFilter /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build.make extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/seqan_flexbar/CMakeFiles/seqan_flexbar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 96%] Built target seqan_flexbar /usr/bin/make -f extras/apps/sgip/CMakeFiles/sgip.dir/build.make extras/apps/sgip/CMakeFiles/sgip.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/sgip /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/sgip /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/sgip/CMakeFiles/sgip.dir/build.make extras/apps/sgip/CMakeFiles/sgip.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/sgip/CMakeFiles/sgip.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 98%] Built target sgip /usr/bin/make -f extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build.make extras/apps/variant_comp/CMakeFiles/variant_comp.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/extras/apps/variant_comp /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/variant_comp /builddir/build/BUILD/seqan-1.4.2/build/Release/extras/apps/variant_comp/CMakeFiles/variant_comp.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/make -f extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build.make extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[2]: Nothing to be done for 'extras/apps/variant_comp/CMakeFiles/variant_comp.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [100%] Built target variant_comp make[1]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-1.4.2/build/Release/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/dfi -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/dfi/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/dfi/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/dfi/example/fasta1.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/dfi/example/fasta2.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/fiona -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/compute_gain -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fiona/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fiona/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fiona/example/reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/mason -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason/example/SRR018294.1.1M.error_dist -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason/example/SRR018311.1.1M.error_dist -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason/example/SRR026674.1.1M.error_dist -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason/example/SRR049254.1.1M.error_dist -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/micro_razers -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/micro_razers/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/micro_razers/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/micro_razers/example/genome.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/micro_razers/example/reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/micro_razers/example/reads.fa.result -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/pair_align -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/pair_align/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/pair_align/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rabema_prepare_sam -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rabema_build_gold_standard -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rabema_evaluate -- Up-to-date: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rabema_prepare_sam -- Up-to-date: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rabema_build_gold_standard -- Up-to-date: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rabema_evaluate -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/rabema/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/rabema/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/razers -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers/example/genome.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers/example/reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers/example/reads2.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/razers2 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers2/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers2/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers2/example/genome.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers2/example/reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers2/example/reads2.fa Change Dir: '/builddir/build/BUILD/seqan-1.4.2/build/Release' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile sak_doc gmake[1]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-1.4.2 -B/builddir/build/BUILD/seqan-1.4.2/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/gmake -f CMakeFiles/Makefile2 sak_doc gmake[2]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-1.4.2 -B/builddir/build/BUILD/seqan-1.4.2/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-1.4.2/build/Release/CMakeFiles 2 /usr/bin/gmake -f CMakeFiles/Makefile2 core/apps/sak/CMakeFiles/sak_doc.dir/all gmake[3]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/gmake -f core/CMakeFiles/seqan_core.dir/build.make core/CMakeFiles/seqan_core.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core /builddir/build/BUILD/seqan-1.4.2/build/Release/core/CMakeFiles/seqan_core.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/gmake -f core/CMakeFiles/seqan_core.dir/build.make core/CMakeFiles/seqan_core.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' gmake[4]: Nothing to be done for 'core/CMakeFiles/seqan_core.dir/build'. gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 0%] Built target seqan_core /usr/bin/gmake -f core/apps/sak/CMakeFiles/sak.dir/build.make core/apps/sak/CMakeFiles/sak.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/gmake -f core/apps/sak/CMakeFiles/sak.dir/build.make core/apps/sak/CMakeFiles/sak.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' gmake[4]: Nothing to be done for 'core/apps/sak/CMakeFiles/sak.dir/build'. gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [ 50%] Built target sak /usr/bin/gmake -f core/apps/sak/CMakeFiles/sak_doc.dir/build.make core/apps/sak/CMakeFiles/sak_doc.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' cd /builddir/build/BUILD/seqan-1.4.2/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-1.4.2 /builddir/build/BUILD/seqan-1.4.2/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak/CMakeFiles/sak_doc.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/gmake -f core/apps/sak/CMakeFiles/sak_doc.dir/build.make core/apps/sak/CMakeFiles/sak_doc.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [100%] Generating README.sak.txt cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak && ../../../bin/sak --export-help=txt > README.sak.txt [100%] Generating sak.1 cd /builddir/build/BUILD/seqan-1.4.2/build/Release/core/apps/sak && ../../../bin/sak --export-help=man > sak.1 gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' [100%] Built target sak_doc gmake[3]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-1.4.2/build/Release/CMakeFiles 0 gmake[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' gmake[1]: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/sak -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sak/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sak/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sak/README.sak.txt -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sak/man/sak.1 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/sam2matrix -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sam2matrix/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sam2matrix/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/samcat -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/samcat/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/samcat/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/seqan_tcoffee -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_tcoffee/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_tcoffee/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_tcoffee/example/seq.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/seqcons -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqcons/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqcons/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/snp_store -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/snp_store/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/snp_store/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/snp_store/example/exampleGenome.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/snp_store/example/exampleReads.gff -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/splazers -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/splazers/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/splazers/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/splazers/example/genome.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/splazers/example/reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/splazers/example/reads.fa.result -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/stellar -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/stellar/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/stellar/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/stellar/example/NC_001474.fasta -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/stellar/example/NC_001477.fasta -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/stellar/example/reads.fasta -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/tree_recon -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/tree_recon/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/tree_recon/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/tree_recon/example/example.dist -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/alf -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/alf/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/alf/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/alf/example/small.fasta -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/breakpoint_calculator -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/breakpoint_calculator/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/breakpoint_calculator/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/breakpoint_calculator/example/alignment.maf -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/bisar -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/casbar -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/four2three -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/bs_tools/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/bs_tools/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/fx_bam_coverage -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fx_tools/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fx_tools/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/gustaf -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf/example/adeno.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf/example/adeno_modified.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf/example/adeno_modified_reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf/example/stellar.gff -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/insegt -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt/example/annoOutput.gff -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt/example/annotations.gff -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt/example/readOutput.gff -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt/example/tupleOutput.gff -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/mason_genome -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/mason_frag_sequencing -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/mason_variator -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/mason_materializer -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/mason_simulator -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason2/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason2/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason2/example/adeno_virus.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/bam2roi -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/roi_feature_projection -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/roi_plot_thumbnails -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/bed_sort.sh -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/gff_sort.sh -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/roi_sort.sh -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/roi_plot_9.sh -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/plot.awk -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/ps2pswLinks.gawk -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/example/dmel.bed -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/example/dmel.gtf -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/example/example.bam -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/R/ngsroi_0.1.tar.gz -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi/R/ngsroi_0.1.zip -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/param_chooser -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/param_chooser/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/param_chooser/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/razers3 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers3/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers3/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers3/example/genome.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers3/example/reads.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers3/example/reads2.fa -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/rep_sep -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/rep_sep/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/rep_sep/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/join -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/searchjoin/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/searchjoin/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/seqan_flexbar -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_flexbar/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_flexbar/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/sgip -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/README -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/iso_m2D_m196.A01 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/iso_r01_m200.A00 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/iso_r01_m200.A01 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/iso_r01_m200.B00 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/iso_r01_m200.B01 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/latin-4 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/lattice-4 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip/example/sts-7 -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/variant_comp -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/variant_comp/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/variant_comp/README make: Leaving directory '/builddir/build/BUILD/seqan-1.4.2/build/Release' + mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/include/seqan + cp -pr extras/include/seqan/LICENSE extras/include/seqan/align_extend extras/include/seqan/align_extend.h extras/include/seqan/align_profile extras/include/seqan/align_profile.h extras/include/seqan/align_split extras/include/seqan/align_split.h extras/include/seqan/alignment_free extras/include/seqan/alignment_free.h extras/include/seqan/bam_io extras/include/seqan/basic extras/include/seqan/basic_extras.h extras/include/seqan/bed_io extras/include/seqan/bed_io.h extras/include/seqan/find extras/include/seqan/find_extras.h extras/include/seqan/find_motif extras/include/seqan/find_motif.h extras/include/seqan/index extras/include/seqan/index_extras.h extras/include/seqan/journaled_set extras/include/seqan/journaled_set.h extras/include/seqan/math extras/include/seqan/math.h extras/include/seqan/misc extras/include/seqan/misc_extras.h extras/include/seqan/parse_lm extras/include/seqan/parse_lm.h extras/include/seqan/roi_io extras/include/seqan/roi_io.h extras/include/seqan/sequence extras/include/seqan/sequence_extras.h extras/include/seqan/statistics extras/include/seqan/statistics.h extras/include/seqan/translation extras/include/seqan/translation.h extras/include/seqan/vcf_io extras/include/seqan/vcf_io.h /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/include/seqan + cp -pr core/include/seqan/LICENSE core/include/seqan/align core/include/seqan/align.h core/include/seqan/arg_parse core/include/seqan/arg_parse.h core/include/seqan/bam_io core/include/seqan/bam_io.h core/include/seqan/basic core/include/seqan/basic.h core/include/seqan/consensus core/include/seqan/consensus.h core/include/seqan/file core/include/seqan/file.h core/include/seqan/find core/include/seqan/find.h core/include/seqan/gff_io core/include/seqan/gff_io.h core/include/seqan/graph_algorithms core/include/seqan/graph_algorithms.h core/include/seqan/graph_align core/include/seqan/graph_align.h core/include/seqan/graph_msa core/include/seqan/graph_msa.h core/include/seqan/graph_types core/include/seqan/graph_types.h core/include/seqan/index core/include/seqan/index.h core/include/seqan/map core/include/seqan/map.h core/include/seqan/misc core/include/seqan/modifier core/include/seqan/modifier.h core/include/seqan/parallel core/include/seqan/parallel.h core/include/seqan/pipe core/include/seqan/pipe.h core/include/seqan/platform core/include/seqan/platform.h core/include/seqan/random core/include/seqan/random.h core/include/seqan/score core/include/seqan/score.h core/include/seqan/seeds core/include/seqan/seeds.h core/include/seqan/seq_io core/include/seqan/seq_io.h core/include/seqan/sequence core/include/seqan/sequence.h core/include/seqan/sequence_journaled core/include/seqan/sequence_journaled.h core/include/seqan/store core/include/seqan/store.h core/include/seqan/stream core/include/seqan/stream.h core/include/seqan/system core/include/seqan/system.h core/include/seqan/version.h /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/include/seqan + mkdir -p seqandoc + cp -pr /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/alf /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/breakpoint_calculator /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/bs_tools /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/dfi /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fiona /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/fx_tools /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/gustaf /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/insegt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/mason2 /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/micro_razers /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/ngs_roi /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/pair_align /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/param_chooser /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/rabema /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers2 /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/razers3 /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/rep_sep /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sak /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sam2matrix /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/samcat /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/searchjoin /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_flexbar /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqan_tcoffee /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/seqcons /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/sgip /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/snp_store /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/splazers /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/stellar /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/tree_recon /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan/variant_comp seqandoc + rm -rf /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan + rm -f 'seqandoc/*.txt' + mv /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/join /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin/searchjoin + find /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/bin -type f -name '*.h' -exec chmod 0755 '{}' ';' + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.4.2-53.fc40 --unique-debug-suffix -1.4.2-53.fc40.ppc64le --unique-debug-src-base seqan-1.4.2-53.fc40.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/seqan-1.4.2 find-debuginfo: starting Extracting debug info from 43 files DWARF-compressing 43 files sepdebugcrcfix: Updated 43 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/seqan-1.4.2-53.fc40.ppc64le 24419 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: seqan-1.4.2-53.fc40.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.IZw1Qn + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + DOCDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan + cp -pr /builddir/build/BUILD/seqan-1.4.2/README.rst /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.HMQIgI + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + LICENSEDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan + cp -pr /builddir/build/BUILD/seqan-1.4.2/BSD.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan + cp -pr /builddir/build/BUILD/seqan-1.4.2/GPLv3+.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan + cp -pr /builddir/build/BUILD/seqan-1.4.2/LGPLv3+.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(gnulib) seqan = 1.4.2-53.fc40 seqan(ppc-64) = 1.4.2-53.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld64.so.2()(64bit) ld64.so.2(GLIBC_2.22)(64bit) ld64.so.2(GLIBC_2.23)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.35)(64bit) libc.so.6(GLIBC_2.36)(64bit) libc.so.6(GLIBC_2.38)(64bit) libemon.so.1.3.1()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_2.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.32)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.2.3)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH) Processing files: seqan-devel-1.4.2-53.fc40.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.J5XRVM + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + DOCDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan-devel + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan-devel + cp -pr /builddir/build/BUILD/seqan-1.4.2/README.rst /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan-devel + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.HbADZo + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + LICENSEDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-devel + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-devel + cp -pr /builddir/build/BUILD/seqan-1.4.2/BSD.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-devel + cp -pr /builddir/build/BUILD/seqan-1.4.2/GPLv3+.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-devel + cp -pr /builddir/build/BUILD/seqan-1.4.2/LGPLv3+.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-devel + RPM_EC=0 ++ jobs -p + exit 0 Provides: seqan-devel = 1.4.2-53.fc40 seqan-devel(ppc-64) = 1.4.2-53.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan-doc-1.4.2-53.fc40.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.RFqD2U + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + DOCDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan-doc + cp -pr /builddir/build/BUILD/seqan-1.4.2/seqandoc /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/doc/seqan-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.mXZWlB + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + LICENSEDIR=/builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-doc + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-doc + cp -pr /builddir/build/BUILD/seqan-1.4.2/BSD.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-doc + cp -pr /builddir/build/BUILD/seqan-1.4.2/GPLv3+.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-doc + cp -pr /builddir/build/BUILD/seqan-1.4.2/LGPLv3+.txt /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le/usr/share/licenses/seqan-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: seqan-doc = 1.4.2-53.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan-debugsource-1.4.2-53.fc40.ppc64le Provides: seqan-debugsource = 1.4.2-53.fc40 seqan-debugsource(ppc-64) = 1.4.2-53.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan-debuginfo-1.4.2-53.fc40.ppc64le Provides: debuginfo(build-id) = 0f0fafb6e98a4c60ee2ba6cd6930d96b5940dafe debuginfo(build-id) = 114a152024cabc79ff724b3f60b47cf75d478e0d debuginfo(build-id) = 1ff1e84ad31e5f16afbccf91a150ea51c1db84c2 debuginfo(build-id) = 21491d859cc35b60095ed6c11c83523fd74e8e7f debuginfo(build-id) = 25c5d77f051ba876a76111050f3261782fee1f07 debuginfo(build-id) = 2e6e91fddc6b01994708e7241a8e5a4b66eafd68 debuginfo(build-id) = 33006d1d0963677fd4d67eff5b6ce88dcbc56505 debuginfo(build-id) = 434c87debdea3506930a155937b94c17567e6afe debuginfo(build-id) = 455129f2ba0d7c590539d0974d3299e4be5354e9 debuginfo(build-id) = 4b04e2032bd916f4e311be3d9ced345c2f18a44f debuginfo(build-id) = 514511664eaecd31fa615274032826cbae816100 debuginfo(build-id) = 5348f3f369079c0a86130f7f6e11aa340c1264d5 debuginfo(build-id) = 610847d382d8298240db5ebb4453e76448039ac3 debuginfo(build-id) = 6e05f62da45500a14dd475bc6eefa504b6d83e8d debuginfo(build-id) = 70dd6202829b33da5460f490a75878e93cfddfe1 debuginfo(build-id) = 720add8700f39e8f421719a236b087ae036a5703 debuginfo(build-id) = 737e9ea3103a29054a48333e566435bc44ad281e debuginfo(build-id) = 77aea42d4903d725971325639a901b944ea77b45 debuginfo(build-id) = 789c04055593d471d7cbb5784ba1f5d20eb300c2 debuginfo(build-id) = 79000ce126f3d575a9264edb5683057eb1816ff4 debuginfo(build-id) = 7b121ccd927ff789ee84643849f99c716c1cfeb8 debuginfo(build-id) = 7ff2b841441cfe01b12d77a5885b7f95ae622177 debuginfo(build-id) = 84a5a62063b3779dc002c38c339398c30bd71d03 debuginfo(build-id) = 865808f5acbed05c759c9dea33af4f98a7094ef9 debuginfo(build-id) = 8e23f4e438446b4698200905eac6a88eabc8400d debuginfo(build-id) = 92909010c6d8cce976ad3b142ee57b2cb203ab5f debuginfo(build-id) = 94353330347f4d4012164b8fc7dd77e18df4a8aa debuginfo(build-id) = aec1ebdca0cbe7b61e2d9c94e81e55c72960b60d debuginfo(build-id) = b037e6b1816d954f5673708acec359693f884226 debuginfo(build-id) = b86b4c5fd2e390c5e8de6406b550e7d375dfc40e debuginfo(build-id) = bfd580a7ced46073d8db4ea1409446d113ad13fd debuginfo(build-id) = c7df060f0035cb0626afefd9b416cb42c204dac9 debuginfo(build-id) = cafe8b9c1e94f8e15dfc4093b67000cedd289ddd debuginfo(build-id) = cb22e4883403a6c42a1d665febd18da8e9a94093 debuginfo(build-id) = cf4a9899eeef530a12886ac6d772884a4a568a14 debuginfo(build-id) = cf8a79ffa374b922da9b1c589ae7cb99ec520eaf debuginfo(build-id) = dc5d3b547e32b571b4e493f51714909a1555950e debuginfo(build-id) = e1e6c97cf43f3f47d7fac05e438deec30477f174 debuginfo(build-id) = e861125b4e26bc5a2fa9dfcd81361763e8687a31 debuginfo(build-id) = ee73b56453211d1178751b1c2a927b1903ed4cba debuginfo(build-id) = f0e0f4f95ead40d1e31d267409d37e810a4fe106 debuginfo(build-id) = f34928bf1377e446ef3f01fca366a654b0026f30 debuginfo(build-id) = fee65f10e87231021125007a25e735678383cac9 seqan-debuginfo = 1.4.2-53.fc40 seqan-debuginfo(ppc-64) = 1.4.2-53.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: seqan-debugsource(ppc-64) = 1.4.2-53.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le Wrote: /builddir/build/RPMS/seqan-1.4.2-53.fc40.ppc64le.rpm Wrote: /builddir/build/RPMS/seqan-debugsource-1.4.2-53.fc40.ppc64le.rpm Wrote: /builddir/build/RPMS/seqan-devel-1.4.2-53.fc40.ppc64le.rpm Wrote: /builddir/build/RPMS/seqan-doc-1.4.2-53.fc40.noarch.rpm Wrote: /builddir/build/RPMS/seqan-debuginfo-1.4.2-53.fc40.ppc64le.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.rfRsMj + umask 022 + cd /builddir/build/BUILD + cd seqan-1.4.2 + /usr/bin/rm -rf /builddir/build/BUILDROOT/seqan-1.4.2-53.fc40.ppc64le + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.yLX2oa + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/seqan-1.4.2-SPECPARTS + rm -rf seqan-1.4.2 seqan-1.4.2.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Finish: rpmbuild seqan-1.4.2-53.fc40.src.rpm Finish: build phase for seqan-1.4.2-53.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-ppc64le-1706322988.398155/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/seqan-1.4.2-53.fc40.src.rpm) Config(child) 54 minutes 35 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "seqan", "epoch": null, "version": "1.4.2", "release": "53.fc40", "arch": "ppc64le" }, { "name": "seqan-debuginfo", "epoch": null, "version": "1.4.2", "release": "53.fc40", "arch": "ppc64le" }, { "name": "seqan-debugsource", "epoch": null, "version": "1.4.2", "release": "53.fc40", "arch": "ppc64le" }, { "name": "seqan-devel", "epoch": null, "version": "1.4.2", "release": "53.fc40", "arch": "ppc64le" }, { "name": "seqan", "epoch": null, "version": "1.4.2", "release": "53.fc40", "arch": "src" }, { "name": "seqan-doc", "epoch": null, "version": "1.4.2", "release": "53.fc40", "arch": "noarch" } ] } RPMResults finished